So today was really the first day that I drove with the new PCM on, now I'm hearing a freaky sound kinda like a vibration right below the firewall, it wasn't there before and I did just put in the plugs also but I don't know why that would do anything. It happens when I get to about 2000r'* but stops after that and before that. It almost sounds like the tranny for some reason.

IO, the only suggestion I could give you is to re-install the original PCM to see if the freaky sound/vibration still exists. The other thing is, and this I'm not 100% sure about, did the the new PCM go through a learn procedure? Were the shift points modified with new PCM?