I had a very similar problem when I put a Mk.2 (short stroke) piston into a friend's TXHC...
I found taking the beartrap off the side of the action helped a bit, but it was still hit and miss with getting the gun to cock and the safety to engage.
I ended up refitting the original piston seal and this solved the problem. Maybe the V-Mach seal doesn't sit as proud of the piston end - effectively shortening the distance that the piston rod is pushed into the trigger mechanism?
Another thing to try would be to replace the cocking shoe... Jim Maccari makes a stronger, tighter fitting version, which may just help the cocking lever shove that piston back just a little further.
Hope this helps.
M.A.D. FOR IT!