You said you heard bad things about SBT. Here's the deal with SBT, best I can tell:
1) About 5-10% of their engines are bad, some with obvious problems/cracks that make you really wonder how they didn't notice.
2) They will communicate and deliver on time. They're a large company, stand behind their products, and will do what they say they'll do. All of the other rebuild shops are small individual shops whose estimates are wildly inaccurate and can be hard/impossible to reach.
3) They use their own re-man parts, some of which other rebuilders won't accept. These parts will be reliable in a stock engine, but will fall apart if you use aftermarket modifications (factory pipe, etc) that increase HP. Many people are unhappy about this.
4) They offer a no-questions-asked warranty and will stand behind it.
5) Get the premium engine. It's the same as the standard but has a longer (2 yr) warranty.
I just had an engine failure on my 96 GTX (main crank bearings failed) and had to replace the engine. I've been very happy so far with my SBT engine, and have had no problems.
P.S. If you do this, you're going to spend more than the Sea Doo is worth. That said, once you do all of this stuff, you've got pretty good confidence that everything is going to just work and you'll have a mostly trouble free ski for many years. If you do the labor yourself, it should cost around $2000, including engine.
I personally recommend osdparts.com for all parts--they've been great, ship on time, know their stuff, and use quality parts.