i used an impact and they came off without to much trouble.
If anything, and you have the trans off (i'm having a hard time understanding your post). Jam a screwdriver in one of the holes om the block, angle it into the teeth of the flywheel...flywheel lock. I use that method when removing the PP.
lets put it this way...the sides of a couple of bolts are grinded down to almost a slant towards the flywheel kinda like this \ and they are like a little tac type looking lol it has SOME bolt patterns on it but its not the full pattern
The last time I was working in there was after one of my disc springs broke and one piece got between the disc and the flywheel and jacked everything up. Every one of the bolt heads was all torn up...I couldn't get a socket on anything. I ended up having to use an air hammer and just pound on them till they broke loose and was able to spin them out by hand.