Intercooler, fill with your choice of parafin, derv (red) degreaser or bioderv/alcohol and leave overnight.
Swill out with degreser etc to get clean, wash and dry thoroughly.
As for the pump, well if it was run standard for a while before the tinkering started then I'd bet you'll see a witness mark on the shaft from the diaphragm that shows where it used to run. If not just turn it back a little until you are happy :?
Once you've seen the description of how to tune it I'm sure you'll be happier with how, it's been discussed many times before with link to that Dosge RAM website, I don't have a link though.
Another thing to check is the boost pressure.