Finally got the last CEL turned off... Fault code D8 the Leak Detection Pump reed switch not open issue. It turned out to be the vacuum line from the Fuel breather valve to the throttle body was disconnected. Also found that one of the grommets under the VCG was missing which contributed to the vacuum leak as well. I believe this is the first time in 5 months I don't have a CEL illuminated in my E46. Thank you Benchmark Motors, you fixed the only issue that stumped me for the last couple of months.