So I replaced bottom seals on both sides where it goes into the intercooler and the upper seal on the red charge air hose.

PITA to get together tight. I've had it apart now three times to re-do it and get the audible clip that every connection is seated properly. Cross my fingers this time is the last time. I installed the red charge hose on the bench just to make sure. Then I fed it all up into position and was able to get a loud click on the other charge line.

I have a CEL code P0299 but I haven't cleared it since the last time I drove it so I'm hoping its just residual.

Can you clear codes on the BMW simply be disconnecting the battery like other cars? I don't have a code reader and many of the parts stores won't reset a code they'll just read it.