As for the 1st boss, I have no clue what causes the crashing yet I also found a fix. I got the original MAP03 and copied this mod's map03 contents. (Lines, Things, Sectors, etc. EXCEPT the MAP03 empty marker!) I replaced the original map03's stuff and saved it as a WAD. Then I imported the WAD in this mod and placed it in the Maps folder. Then it just... Worked? I don't know why. Maybe because the MAP03 Marker was just Empty in this mod instead of it being the thing that shows you the map? Either way, I did the same process to all the other maps just in case any other issues popped up with them.
~MSF