The rods can follow the crank, for as much clearance the small end, has inside the piston bosses. I'd look inside the pistons for signs of that.
But, if the limit of axial travel was exceeded, I think all the rods would show it and be discolored, at the big end.
If the rod clearance was in spec, for the load range, I'd follow that crank passage back to the main bearing.
Could it be that that the crank pushed far enough forward, that it covered up most of the feed hole to the pin?
No matter what, the end play issue, has to be fixed before it's put back together. I'd suggest mounting the face of the block to a eng stand, put in a good used thrust bearing, crank and FW on, then put the trans on a table at the same height and push them together to find, when and where they bind. Start with 1/8" thick washers and reduce the space, until ii binds.
My guess is it the shank that drives the pump having no end play. Nothing can give between the converter mounting pads and the end of the pump drive.
You can also put a indicator on the flex plate as you tighten the bell housing bolts, to know when it starts pushing the crank.