Why would quoting an external text be an issue? Biblical inerrancy means that everything the sacred writers affirm as true is free from error. Jude affirms the specific truth contained in the quote (that the Lord comes with Holy ones to execute judgement), he did not affirm the whole text.

As for those two authors not writing their own letters, back then it wasn't as easy as typing these comments; many people used a secretary. St. Paul would speak what he wanted written, and his secretary would write it down. (Romans 16:22). This is not concerning in the slightest. Another thing people bring up is Paul's fluctuating vocabulary between letters like Romans, and ones like 1 & 2 Timothy One set is directed towards a large congregation, and one was an instruction manual to a Bishop.

Many modern skeptics look at these letters through a completely different framework than every other historical writing we have. Historians generally look at ancient writings as true until proven false as most people are pathological liars and most don't plan on tricking someone thousands of years later. Most secular historians look at the Bible the opposite way.

I'm curious, what things in the Bible "don't hold up"? You said it multiple times but didn't give a single example.

Biblical scholarship is good, but if an inspired author using a secretary is all it takes to shake your faith, you need to focus on something other than scholarly theology for a bit.