I've got the same Probe pistons but mine are .030 I have a Eagle cast 4" crank too . I haven't put the motor together yet so I'm very interested in your outcome! Maybe I'll call Probe and ask them if they're aware of this issue.
That's a good idea. Call the source. Something isn't right. I know sometimes you have to trim a bit off the block, but shouldn't have to trim anything off the crank for clearance. I'd be interested to know how this problem is solved also.