I too had the revving thing going on with mine, about the second year I owned my proton. It would inexplicably rev up and this would cause it to be difficult to engage a gear (from start), or it would go the opposite and idle as such a low RPM that it would stall in when stopped at a light. I'm not sure what I did to fix it - but it seems like changing the gas filter and cleaning out the EGR had a huge impact (plus running some injector cleaner through the gas - I also changed to mid-grade fuel - 89 octane in these parts). After a while it just went away, but it might be due to my being more cognizant in taking care of the truck. Back when my Toyota would act in a similar fashion, a thorough cleaning of the throttle body seemed to fix it right up for 6-8 months or so, then I would have to take it apart and clean it out again.
While removing the old plenum to install the super charger, I noticed tons of gunk in the cylinder heads (along the edges where fuel didn't hit with pressure), the inside of the plenum, the throttle body and all along the intake pipe. I hadn't disembled everything like that before so it was an eye opening experience. We cleaned everything thoroughly before replacing with the alpine manifold and the SC aside, it seemed to be breathing better. After reading about the new torque setting for the intake manifold I can understand why the intake gaskets leak - the SB shows much less torque than what is indicated in manuals, and they probably came from the factory over-torqued. Since they are phenolic with thin metal sleeves, even a slight over-torque could cause something to fail - my guess as to why the setting was reduced. It might take the removal of the plenum and a good cleaning, but at minimum I would try a few things: replace gas filter, clean EGR (replace gasket), replace PCV and fill up with good gas with an injector cleaning additive - that should address the revving/dying issue. If that doesn't fix things, try cleaning the Throttle Body and and doing a tranny flush with filter exchange (might want to do that anyway if things are shifting poorly). Finally, taking off the plenum, cleaning everything out well and replacing the intake manifold gaskets should wipe out all those as potential causes of your issues. If I was closer I would bring John Schellenberg over and we'd give it a once over - otherwise it's a bit of a haul from Atlanta.
-- John