So the decreasing load and fueling issue is indeed directly related to setting the IMRC System Switch to "0".
This is what I changed (or not) in my tune to compensate for installing a new intake manifold with no flaps. You may be able to get away with leaving the spark tables alone, but personally I like to know exactly where the total spark value is coming from without guessing whether or not the PCM is actually adjusting for IMRC.
1) leave the System Switches\Scalar\IMRC Switch at "1"
2) Add the IMRC\Spark Adder to Borderline for IMRCs values to the Spark\Borderline Knock\Borderline Knock Table
3) Zero-out the IMRC\Spark Adder to Borderline for IMRCs values
4) Add the IMRC\Spark Adder to MBT Table for IMRCs values to Spark\MBT Spark\MBT Spark Table
5) Zero-out the IMRC\Spark Adder to MBT Table for IMRCs values
6) leave IMRC\IMRC Opening RPM as-is. This seems to no longer have an effect, as the "imrc open" flag is always "1" now in the logs, even at idle.
There are some tables under "Transient Fuel" which I did not touch.
I will update this thread if I feel there is anything else to add.
In closing, I will say that I DO NOT KNOW exactly why the PCM 1) negates the load calculation at the IMRC Open RPM position and 2) pulls fuel like crazy by setting the IMRC Switch to "0". Until I hear an explanation I am going to assume it is a bug in the SCT software.
2006 sonic blue zx5 GT2871r turbo.