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I just saw your post and it reminded me of engine swap a buddy did a while back.
I cant tell for sure, but your flywheel bolts look new. I hope you got flywheel bolts for a flywheel and didn't reuse the flexplate bolts? The flex plate bolts are about 1/4 - 3/8" shorter than they need to be for a flywheel.
What diameter is your brake booster? It seems to be smaller than a stock 9"?
Flywheel bolts are brand new for flywheel. Flywheel resurfaced. I bought all new grade 8 bolts to mount bellhousing, transmission, etc.
My brake booster and master cylinder are stock replacements - brand new. Good to go!