I went from a TH700-R4 to T56 back in 2001 and wouldn't go back to auto.
I'll concede that the auto was more fun at the drag strip, but autox and road course are much more fun for me than drag racing.
No imaginable reason why a manual trans would interfere with inspection.
I wouldn't recommend a T5 with your engine, unless it's an upgraded version that can hold up to the extra output.
You'll want a chip with manual-trans calibration, or your idle will be funky. Come to a stop, idle hangs at ~1500rpm for a few seconds before returning to normal.
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1982 Z28 w/ '01 LS1 + T56, TR224 cam, Katech oil pump, JWIS chain
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