I definitely feel your pain as I'm going through a similar situation with my 2001 Nissan Frontier at the moment. Paid $3500 for a reman swap and got an "overhaul" instead. First time they dropped it off I tried to drive it back to work and it broke down within the first ten miles. Cost $300 to have it towed back to my garage. That weekend I went over my newly "overhauled" engine. Other than a cheap aftermarket distributor, not a damn thing had been done to it. Same Pistons, rods, rod bearings, belts, etc.. In fact, the damn thing still had the original valve and intake gaskets that I put on prior to sending it to the shop (I always initial new parts I install out of habit). Long story short, I called for a refund, but he asked for the chance to make it right first, which I agreed to. He told me it was done and would be dropped off today, so we'll see. After learning that I'm not mechanically retarded, I'm hoping I scared him into installing a new factory motor, but I'm not holding my breath.
Most likely I'll just end up similarly eating the cost of this failed endeavor like you.
The TL1000R is the only bike that makes me nervous, because in my dreams it's the only bike I die on