MSPNP1 or MSPNP2?
Just gave a bunch of advice over here that might help you:
Tuning Help Required
I agree that the signals look noisy, so you should check that you are using good, secure common grounds.
Idling rich and going to a lean stumble off-idle is what I experienced with the MSPNP basemap also. But it was easily tuned away.
You need to understand the function of the VE and AFR tables. The Megasquirt operates primarly from the VE table. During steady state under certain conditions (for example NOT when under boost), the Megasquirt will automatically adjust to try and achieve the AFR table. BUT, the amount of adjustment available is limited -- typically to no more than a 5%-10% change. If you've got a MSPNP1, this is found in the "Exhaust Gas Settings" dialogue. Why the limited authority? Consider what could happen to your engine if the WBO2 had a failure and fed a false rich to the MSPNP.
If your VE table is way off (and if you're still using the initial basemap, you are way off), then I recommend that for the first couple of tuning iterations you use MegaLog Viewer's VE analyzer function. That way, you can see the recommended changes and make sure they're sensible. Once you're closer, you can start using TunerStudio's autotune function.
Be patient. It works . . . well.