Couple different things going on here, actually:

"connections" to "connexions", changing "Muslims" to "Moslems"

"Connexions" and "Moslem" are somewhat archaic spellings, some of which were common in English right up through the late 20th century, though "connexions" is a bit of an older version - H. P. Lovecraft, who enjoyed peppering his letters with 17th century spellings and Britishisms, was fond of "connexions." "Moslem," like "Hindoo" and similar terms began to fall out of fashion as the more contemporary forms were introduced (as more accurate translations or less likely to be mispronounced), usually starting in academic circles and spreading out through newspapers and dictionaries. Like a lot of archaic bits of speech, it's still present here and there. You might want to check out A History of the English Language: Revised edition, chapter 8 "Modern Language" for more backstory on those kind of developments.

inclusion of diphthongs like æ

While this is a diphthong, it's actually also something much more critical to typesetting: a ligature, where two different letters are combined into a single symbol. You used to see a lot more of these in the days of movable type, but they became less necessary as printing moved away from movable type and into more advanced printing methods, so they were largely dropped - although that's a bit simplistic, and symbols like the ampersand, "&" which began as ligatures remain very common. You might check out Typography & typesetting: Type design and manipulation using today's technology for more on how ligatures are still relevant in today's typography.

Was spoken English different from when these books were printed (e.g. people really pronounced it mOslEms). Or were these artifacts from their original translations that got ironed out later?

Little bit of both. Archaic and alternate spellings, regional dialects, diphthongs, ligatures, etc. are still with us in English today - contemporary English readers can still read an English work printed in the 17th century - and these things pepper our speech. The difference in pronunciation between "Muslim" and "Moslem" is still an issue today.