I used the starter that came on my L33 (2006 Silverado) as well. I had to grind a significant portion of the dome off, but it eventually fit.
I've had incredibly poor results with every single aftermarket starter I've ever used in terms of casting quality of the housings. It's difficult to find a more sturdy starter than a good 'ol GM truck starter. Also, I would have scrapped the starter anyway if if didn't fit, so it's a win-win all around.
As for the timing cover bolts, I replaced all the original hex head bolts with countersunk allen head bolts. I opened up each hold on timing cover with a beveled drill bit and the new bolts sit almost flush with the surface of the timing cover.
I love the progress updates from you and J. I went a different route with the motor mounts and fabricated my own design and omitted the longitudinal pieces that connect the front later bar to the middle lateral bar. My mounts land squarely on the front cross bar.
I was also able to reuse the stock transmission mounts. I made spacers out of the original trans brackets that offset the Renegade bracket to the OEM mount. Everything seems to mount up.
(cell phone pic, it's the best I got. Sorry)
(full size)
I'm currently stuck in wiring hell at the moment. I'm trying to keep the electronic throttle body / drive by wire form the original truck motor. It's been... challenging. There is little to no documentation online on what is compatible with what, and I was never given the original throttle controller when I bought the engine. I'm on my THIRD throttle body controller and I STILL can't get the goddamn module to talk to the ECU. It powers up for ~5 seconds, doesn't see any UART comm from the ECU and then eventually shuts off. Frustrating.
At this point, I'm probably going to drop the engine and restart a new harness for everything from scratch. Any resources you may have for harness info is appreciated.
-A