Robb,
We've wrestled with the same puzzle. For now, we've decided to live with the original configuration. Our spillover is 12"-13" above the waterline depending, I think, on who is measuring and whether we have an extra case of beer on board (just kidding). Anyway, at that height, we're borderline safe, and we were able to reconfigure the exhaust hose this past spring to get some downhill pitch on it between the wet elbow and the elbow where it turns to meet the muffler.
Like you, we had to replace the turbo and exhaust elbow. The damage preceded our purchase of the boat in early 2012. We did the work in early 2014. Like you, we had extensive consultations with Tony about how to proceed, and we decided that the simplest solution would be to top-mount the turbo and raise the engine box. We talked to our fiberglass guy about how to proceed, and he'd be inclined to remove the trim piece on the bottom of the hatch and add material to increase the height. At the joint of old & new, he would install a new aluminum half-round trim piece. The existing bottom trim would be reinstalled on the (new) bottom edge. He said he could also eliminate the trim piece at the joint and make the new fiberglass match the old. That would add 5-6 hrs. to the job.
We've now been through two seasons since replacing the turbo, and at the end of each season, we have pulled the exhaust elbow to look at the turbo. It's doing just fine so far. Of course, being in a fresh water lake doesn't hurt a bit.
I really appreciate the brainstorming that happens on this forum.
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