Alright, got myself a mityvac and tested the modulator line. Seems fine, however everything I tested with the vac seems to have a slow leak, even if I test a plugged line off the car anything under 20" slowly looses the vacuum but if I pump it up to over 20" it holds. Could the mityvac be faulty? I hope not as I just bought the thing!

I found a big leak, as I couldn't even pump it up over 5", at the switch over valves on top of the valve cover, replacing the vacuum lines there fixed that. The next big leak was at the EGR itself and the switch that is just before the EGR. I plugged the line leading to the switch and test drove the car. Much better! Downshifts are much smoother. I'm going to replace the rubber "t" fittings and get some new plastic vacuum line from the dealer. You're right about them being full of carbon. Is it O.K. to run the car with the line to that switch plugged? I assume it's a switch for the EGR valve? Thanks!