Ok it sounds like you have multiple problems to me.
This site has a basic explanation of the govenor and the vacuum modulator about half way down. The FMX only uses throttle possition for high load downshifting(passing gear).
The modulator is on the rear left side of the tranny. Take a real close look at the rubber hose on the bottom, trace the line up and make sure it is attached to the vacuum T on the back of the intake manifold, make sure the rubber is not cracked or leaking and that it is hooked up properly. Work was done in that area and the line might have been knocked off.
You say in your sig that you have a mild cam. Most mild cams will still produce enough vacuum to operate the modulator. However if you have a vacuum leak and a cam then you might not have enough vaccum. Spray the intake down with carb cleaner to make sure you dont have any vacuum leaks.
Double check your transmission fluid is full when the car is idling and engine hot.
The gray build up is from the clutch packs and is perfectly normal to have soem in the pan. Wouldnt be a concern to me unless there is metal chunks or the fluid has a burnt smell.
I would say that after you have covered the basics with fluid, modulator hooked up and good vaccum then i would say it is time to head to a tranny shop so they can look at possible sticking servos, band adjustment, etc...
The speedo fluxing is most likely from the new gear being modded to fit.