Sounds like the up pipe donut gaskets are failing with the extra soot in the engine bay. That would certainly contribute to the extra soot out the tail pipe as well. Leaky up pipes=less drive pressure=less boost to clean up the fuel. Turbo might likely still be ok.
Regardless, the gt38r seems to be a good drop in turbo upgrade. Nearly all talk about housings are on the exhaust/turbine side. Just did some looking on bean's diesel and saw that they offer the gt38r with the 1.0 wastegated housing or the 1.15 non-wastegated along with the necessary adapter flange to get to the downpipe. I haven't run the gt38r period, so I can't give any impressions with either housing, but if your doing more higher rpm driving and can handle the slightly reduced lag you'd probably be better off with a larger housing. Stock is .84 so you'll be getting the getting the benefits(reduced egts/backpressure) of a larger housing even if you stick with the 1.0 that the gt38r comes with. Spool up with the larger housing 1.0 gt38r is probably quicker than stock just because of the ball bearing design, but I can't say for sure without driving one.
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Thomas H.
'97 F-250 CCSB 7.3L Auto, Gauges, Modded H2E, 285/200% sticks, 7.3L IC, Stealth Dual HPOP, Pheonix chip
'03 F-250 CCSB 6.0L Auto, Gryphon CTS, FICM tuning by PHP, Powermax
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