Going from memory, as it's been a few years since I've seen mine (though hopefully I will get it back, someday). when I refinished mine, it took a fair bit of work to get everything to play nice, the front standard and the rear should be dead flat against the carriers. as pointed out by Leslie, because they're stamped, they tend to cup slightly.
I used a sheet of 320 grit sandpaper on a sheet of thick plate glass, spray some water on the glass, lay the sand paper down, spray a little more water and start sanding. once the surface is flat (indicated by total contact with the sandpaper) go to 400 grit for a little bit, then 600.
I also found that the carrier wasn't perfectly flat, and a few mins with the 320 solved that.
if you're not using rear tilts, you want all 4 knobs in the rear standard. since you don't have them, go to the local woodworking store and find some knobs with 1/4-20 threads (from memory, could be wrong) go ahead and get 4, the combination of smoothing and 4 bolts should clear up most of the issues.
as far as the fit between the guides and track, some very judicious bending and tweeking will solve that, just be aware that aluminum work hardens when you bend it, and it takes a fair bit of heat to re-anneal. Out of curiosity, is it rigid when you flip the lock?
erie