I decided to take a crack at a transliteration (I need the practice). I know one exists by Neal but I haven't really looked at it. I have sampled some of the alphabet in the original letter to record the script style.
So... I don't know how much this diverges from Neal's transliteration and I am not strong at Latin, but my script-interpretation skills (ability to read old letter styles) is reasonably good, so take it for what it's worth:
Transliteration:
R[evere]nde/R[everen]d[ißim]e in Chr[ist]o P[ate]r D[omi]ne et Amice observandissime
Scripsi R[evere]ndae P[ate]r[ni]t[a]ti V[est]ra Ratisboná ea, que mihi á R[everenda] P[aternitas] V[est]rá fuerant commissa, apud Caes[eream]
Maiestatem ex voto transegisse. Confido meas literas ab Illustriss[imis] Comitibus de Martinitz,
ad quos Ego direxi, recepisse. Et cum sex hebdomade praeterierint, responsum cum vesiverio/desiderio [1]
expecto. Scripsit mihi R.P. Gans RP. V' nescio quas persecutiones habere. quod cum
nimis generite dicatur, me valde solicitum reddidit. Et cum quidam ex his s?i?e [scire??] intersis,
transcripsi partem Epistole. Illustriss[imus] Comes Bernardus dolenter mihi fuit questas
nihil responsi ad suas literas obtinuisse. Ego cum multis beneficiis/beneficÿs ab eo sim affectus,
sciamq[ue] studiosissimum esse Rev[eren]dae P. V[est]rae, neq[ue] parum fecisse apud Caesaream Maiestatem, quod
e re nostra sit futurum, optarem gaudere de aliquali benevolentiae et mutui affectus declaratione.
Sili modo que Amicus meus M. Georgius Barschius per me scribi voluerit, et sch?dala/schzdala/schgdala/schyvalá [2]
hie/hic adiuncta intelliget. Est certe vir optimus et rerum chymicarum peritissimus, verum
desideratum finem necdum assecutus; quem non auri sed Medicinae gratia tam solicite quaerit
Caesarea Maiestas admodum curiose de illo heliotropo et me quaerebat, an illud nossem,
vel saltem effectum effectum vidissem. negavi utrumq[ue] : Mirantiq[ue] dixi abuti?/abate? non faisse ausum [3]
incipiente tum primum Amicitia, atq[ue] illud petere quod pro secreto maximo haberet. [4]
Si in aegre non ferat, et in specie dici non[ ]expedit [5], rogarem in genere duntaxat rescire
resne sit naalis[6] an factitia, mineralis an vegetabilis, et an in nostra Patria repertibilis.
Quidquid dictum fuerit, servabo sub eodem sigillo [7], quo fuero obligatus. Praeterea
peto descriptionem illius atramenti variegati et succulabo, utramq[ue] Romae mihi promissum.
Si quid praeterea scita utile, addere non gravetur. Sed et illud significare an lexicon
Copto Arabicum cum literis Arabicis sit excudendum. Ursi proximis literis matrices illas
oreontalium [8] literaru[m] quam primum exculpendas: ut si forte hic quid sile esset edendum,
nobis non desint necessaria instrumenta. Hisce precor R. P V[estr]am quam felicissime valere
et quam citissime nos invisere. Dignetar Salutare R P. Ferrariu[m] et signi praeterea
novo[ ]er[un]t [9] suum servum Joannem Marci.
Pragae 12 Septemb. anno 1640
Notes:
[1] I would like to read this as desiderio, which is a more common word, but the scribe doesn't typically write "d" like this except for the words "illud" and sometimes "quid", the d usually has a long straight stem. Vesiverio is also a Latin word, just older and less common. It seems odd that the scribe would use a completely different shape for "d" here. The letter "v" at the beginnings of words was quite often written like this, with a long back-swooping tail, but not usually so rounded. If it's "d", it's an odd departure from style but in this context desiderio seems more likely.
[2] I can't make sense of this, but that second-to-last letter isn't written like the usual "t", it's longer and has no cross-stem. It's also hard to tell if the line over the last a is an accent or an abbreviation symbol (the scribe uses the mark both ways). If this were an English scribe, the 4th letter would be "y" (the curved-right tail is commonly found in Anglicana) but it doesn't appear to be an English hand in any other way, so I'm not sure what letter it is, surely not g or q, maybe z.
[3] non faisse is used in Latin, and the scribe has written the letter "a", but this particular expression is more commonly written non fuisse ausum
[4] The z at the end would indicate an ending like -um or -rum but this phrase is usually written "maximo haberet", so I'm not sure why the z is there.
[5] This appears to be written as expedix but I'm sure expedit was meant.
[6] I don't know what naalis is and there's no abbreviation mark, but when naturalis and factitia are combined, the writer is usually referring to something that might be real or fictitious, so perhaps it is na[tur]alis.
[7] I can't tell if this is written as silligu[m], sigillo, or silliga (plural) as it looks more like a "u" but the difference isn't significant since they all mean "seal".
[8] This looks like it's written oreontalium, but I assume it means orientalium.
[9] This is hard to read, but I think it's possibly meant as novo erunt except that it's written as one word (and abbreviated). Not sure, though.
So... I don't know how much this diverges from Neal's transliteration and I am not strong at Latin, but my script-interpretation skills (ability to read old letter styles) is reasonably good, so take it for what it's worth:
Transliteration:
R[evere]nde/R[everen]d[ißim]e in Chr[ist]o P[ate]r D[omi]ne et Amice observandissime
Scripsi R[evere]ndae P[ate]r[ni]t[a]ti V[est]ra Ratisboná ea, que mihi á R[everenda] P[aternitas] V[est]rá fuerant commissa, apud Caes[eream]
Maiestatem ex voto transegisse. Confido meas literas ab Illustriss[imis] Comitibus de Martinitz,
ad quos Ego direxi, recepisse. Et cum sex hebdomade praeterierint, responsum cum vesiverio/desiderio [1]
expecto. Scripsit mihi R.P. Gans RP. V' nescio quas persecutiones habere. quod cum
nimis generite dicatur, me valde solicitum reddidit. Et cum quidam ex his s?i?e [scire??] intersis,
transcripsi partem Epistole. Illustriss[imus] Comes Bernardus dolenter mihi fuit questas
nihil responsi ad suas literas obtinuisse. Ego cum multis beneficiis/beneficÿs ab eo sim affectus,
sciamq[ue] studiosissimum esse Rev[eren]dae P. V[est]rae, neq[ue] parum fecisse apud Caesaream Maiestatem, quod
e re nostra sit futurum, optarem gaudere de aliquali benevolentiae et mutui affectus declaratione.
Sili modo que Amicus meus M. Georgius Barschius per me scribi voluerit, et sch?dala/schzdala/schgdala/schyvalá [2]
hie/hic adiuncta intelliget. Est certe vir optimus et rerum chymicarum peritissimus, verum
desideratum finem necdum assecutus; quem non auri sed Medicinae gratia tam solicite quaerit
Caesarea Maiestas admodum curiose de illo heliotropo et me quaerebat, an illud nossem,
vel saltem effectum effectum vidissem. negavi utrumq[ue] : Mirantiq[ue] dixi abuti?/abate? non faisse ausum [3]
incipiente tum primum Amicitia, atq[ue] illud petere quod pro secreto maximo haberet. [4]
Si in aegre non ferat, et in specie dici non[ ]expedit [5], rogarem in genere duntaxat rescire
resne sit naalis[6] an factitia, mineralis an vegetabilis, et an in nostra Patria repertibilis.
Quidquid dictum fuerit, servabo sub eodem sigillo [7], quo fuero obligatus. Praeterea
peto descriptionem illius atramenti variegati et succulabo, utramq[ue] Romae mihi promissum.
Si quid praeterea scita utile, addere non gravetur. Sed et illud significare an lexicon
Copto Arabicum cum literis Arabicis sit excudendum. Ursi proximis literis matrices illas
oreontalium [8] literaru[m] quam primum exculpendas: ut si forte hic quid sile esset edendum,
nobis non desint necessaria instrumenta. Hisce precor R. P V[estr]am quam felicissime valere
et quam citissime nos invisere. Dignetar Salutare R P. Ferrariu[m] et signi praeterea
novo[ ]er[un]t [9] suum servum Joannem Marci.
Pragae 12 Septemb. anno 1640
Notes:
[1] I would like to read this as desiderio, which is a more common word, but the scribe doesn't typically write "d" like this except for the words "illud" and sometimes "quid", the d usually has a long straight stem. Vesiverio is also a Latin word, just older and less common. It seems odd that the scribe would use a completely different shape for "d" here. The letter "v" at the beginnings of words was quite often written like this, with a long back-swooping tail, but not usually so rounded. If it's "d", it's an odd departure from style but in this context desiderio seems more likely.
[2] I can't make sense of this, but that second-to-last letter isn't written like the usual "t", it's longer and has no cross-stem. It's also hard to tell if the line over the last a is an accent or an abbreviation symbol (the scribe uses the mark both ways). If this were an English scribe, the 4th letter would be "y" (the curved-right tail is commonly found in Anglicana) but it doesn't appear to be an English hand in any other way, so I'm not sure what letter it is, surely not g or q, maybe z.
[3] non faisse is used in Latin, and the scribe has written the letter "a", but this particular expression is more commonly written non fuisse ausum
[4] The z at the end would indicate an ending like -um or -rum but this phrase is usually written "maximo haberet", so I'm not sure why the z is there.
[5] This appears to be written as expedix but I'm sure expedit was meant.
[6] I don't know what naalis is and there's no abbreviation mark, but when naturalis and factitia are combined, the writer is usually referring to something that might be real or fictitious, so perhaps it is na[tur]alis.
[7] I can't tell if this is written as silligu[m], sigillo, or silliga (plural) as it looks more like a "u" but the difference isn't significant since they all mean "seal".
[8] This looks like it's written oreontalium, but I assume it means orientalium.
[9] This is hard to read, but I think it's possibly meant as novo erunt except that it's written as one word (and abbreviated). Not sure, though.