That's what I've been saying all along use the MEMCAL that has an original configuration for the induction system, in this case, CPI. Then program an EPROM for CPI with a manual trans, don't worry about what the original PROM was programmed for, it becomes null and void in the end. The LHM and RFD (and knock filter) side of the MEMCAL are the parts that remain connected to the ECM in the end. Even if there are large changes between an auto cal and a manual cal, there are editors for that (Tuner Pro). ;)
No, you can't use the TBI PROM on the CFI MEMCAL to accomplish what you want. The BIN/PROM is still programmed for TBI and will at the very least pop up a CEL (Check Engine Light) for cyl count error, possibly MEMCAL or PROM error.
The solution is simple. Use the CPI MEMCAL and program an EPROM with a CFI and manual trans bin. I'm pretty sure you will need to set-up the CPI bin for manual yourself, I don't recall there being a CPI with a manual trans from the factory.
You can use the compare function in Tuner Pro to find differences between auto and manual bins. Some stuff that would be TBI specific you would have to ignore.
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