Saying Jesus would not have agreed with Paul is problematic being that Paul had no interest in a historical Jesus. He was interested in the Christ of his vision. Paul does not appear to know anything about a historical Jesus or he does not care.

There was historical school and it appears Paul might have been at war with them (Gal. 1:6-9 and 3:1-3).

It appears the Church simply incorporated two entirely different strands--the historical Jesus and the mythical Christ--and put their writings into one book while revisioners over the decades and centuries revised and smoothed the gaps as they saw fit (often leaving bigger gaps than the ones they tried to fix).

Paul's rapture scenario is also problematic in that he never wrote it again in any other of his epistles.

As for the thorn in his flesh, there is good evidence that it may have been homosexuality.