I think the original poster has the big holes in the plate, and the small holes in the converter.
That said, options are
replace flexplate
replace converter
or drill converter, and tap to larger size.
In all honesty, I had a van I put together with this combo, and just put it together as is(small bolts through the larger holes in the flexplate)
It never gave me any trouble. I'm not saying I would run it like that now(I would correct the problem), but I do think it is not as big of a concern as it would seem.