You mentioned the engines are running much better than stock after modifications, several things are happening.

More performance does mean more forces. The piston has already to deal with a lot of G-forces and every extra bit of performance is dubbeling the load. A thin part like the skirt is the weakest part of a piston. Just for fun calculate the speed of the crankpin turning arround at top RPM, it can go up to 100 km/u, The piston is accalerating from 0 to 100 km/u in an half stroke and slows down to 0 in the other half stroke. The G-force on a few grams piston can go up to several kilograms.....

Then there is flex in the crankshaft, with more RPM the bending of the krankshaft is getting larger and it is possible that the skirt is touching the backplate or the piston is even touching the head, if that is the problem you should see a mark in the backplate and/or head.

And a last thing is heat. The skirt has to deal with a lot of heat and heat is affecting the strength of materials. It becomes weak and can deform or snap off due the high forces. In this case some extra cooling with better lubrication can do the trick.

Some things to look at.....