I talked to John Cope and he recommended that I surface grind the bolts, chase threads. He said washers could work but they would have to go between the flex plate and converter otherwise the heads could contact the motor.
He seemed surprised that they bottomed out but understood the problem. I pick up my flex plate tomorrow and will get to work on it. Now I wish I had trial fit everything when I got it in. Hope it all comes together, I at least need the motor in this weekend.
Edit: This is for a mild street build. 9.2-1, bigger cam, head / valve work, headers, lower gears, 4 bbl. TC is around a 2400 2500 stall.