I grabbed the NA motor UIM failure before having a chance to notice the section you posted this into. I would doubt you have any head or LIM issues beyond a gasket or o-ring. Most likely when you put the charger in place, one of your o-rings moved. Being that you don't mention your year, I'm guessing 97-03 as the o-rings were simply sitting in place and not held or molded into the gasket like the 04+ years.

Only other thing I'd think it could be would be the end seal on the LIM, it's a little cover under the TB with two 8mm bolts. This cover