I've got a couple suggestions....

Check the air gap between the ckp sensor and the trigger wheel. Also, you mentioned that your pulley is wobbling. You may want to remove it and check that the keyway isn't worn from improper torquing of the front crank bolt. The trigger wheel is bolted to the pulley, so if it's wobbling around it could certainly cause issues with improper spark timing, probably more noticeable at idle/lower rpm.

Switch the MAF sensor with a known good one, I believe that is your problem.
And check wiring to the MAF sensor as well, just to be sure nothing was tampered with with new Intake...

All good suggestions, will try when i get a minute.

When do you get backfires out the intake?
I get a backfire out the intake when I turn the key to "ON". If I have the throttle open it sounds like a gun being fired.
When this happens it tends to be hesitant and rough on low rpm, until it warms up. Is your rough running consistant no matter the conditions?

Curious if you're having the same issue as I am.

/\ Mine does that occasionally too. Are you still on the stock ecm? I've found that when you "key on" all four plugs spark at the same time once. I always figured it was either some un-burnt fuel remaining in one of the cylinders on last shut down, or a slightly leaky injector that filled up one of the cylinders until all the fuel pressure has bled off.

I could be completely wrong but it seems to make sense.:dunno:

Ecm? Im on stock ecu if that's what u mean.
Before I leave I normally hold the accelerator open to let it air out a bit. It seems to help a bit but it can be time consuming. I always assumed it was a leaky injector. Im changing out the injectors when I install my ms3 and hoping that fixes it.