I want to say that I can empathize with your situation and I hope it works out for you. I recently went through the mechanic selection when my 2006 HPDI blew Cylinder 1 and researched many options, before I made my selection on mechanic. I also contacted Texas Outboard Motor Rebuilders and they did inform me they stopped doing HPDI rebuilds. What I discovered, was most mechanics I spoke with were offering 3-6 months warranty on their work. I was very close to selecting Hydro Tec and had multiple conversations with them. They were very pleasant and customer oriented; answered all my questions. I had reservations on making the 13-14 hour drive to Missouri from San Antonio, so I made another selection, which offered me a One year warranty like Hydro Tec. Unfortunately, my rebuild experience did not work out for me and after two unsuccessful rebuilds, I decided to purchase a new in box 2016 Yamaha SHO. Looking back at it retrospectively, and if I could do it over again for the rebuild, I would have made the drive to have Hydro Tec do it. I have been informed by many that Hydro Tec does the rebuilds for Yamaha.
My last discussion with them was in August 2016. From my recollection, the rebuild was going to be around $5800, if your block was in good shape and could be credited as a core charge. Hope I worded that right. The great thing is you have to give them about 3 weeks lead time, so they can prepare your remanufactured power head and schedule a day for drop off. If you drop off your boat on Monday morning, it will be ready next day with the break in complete. They have a Dyno machine and they go through your entire motor. I researched a new powerhead from Yamaha, and at the time it was around 8K with a one year warranty as well.
I wish you much luck in finding the optimal solution to your situation. If you are like me, being on my boat is my sanctuary and allows me to decompress, so when I was without it, it made me realize how much I value having it operational. http://www.yamaha-rebuild.com/