I think you already paid about $600 for the Scat crank that is giving you the problem. If they want almost another $1500 for a complete 462 stroker kit that puts you around $2100. That’s about the going rate on the kit so I don’t see a huge savings. I guess you didn’t say if they were letting you keep the crank your having problems with, if they are then it’s not a bad deal.
I also don’t quite buy the deal that aftermarket pistons are required......, 3 years ago I bought a Scat 462 stroker kit that come with Mahle pistons and had the same issue, crankshaft counterweight hitting the piston pin boss. I was working with Barry and he took care of it for me by getting a different crankshaft. Seems Like I still keep hearing about this problem popping up. I think you need to have a heart to heart talk with whoever supplied the crankshaft.
Hang in there and post end result.