My 93 325i has been sitting for two years when i ran it the other day it seems two only have 1st,2cnd,&rev. but did not have this problem when I parked it. I checked the tranny fluid it's full. any ideas?

Perform ODBII scan. Look for speed sensor fault. Trans has to read speed to know what gear to engage. Could also be a governor problem. Try shifting from low to high gear manually

If it is a standard transmission, might be your linkage is bent or gummed up or may need lubed, or it could be in need of a new throughout bearing, if it is an automatic a pump internally might be malfunctioning

After for setting for so long it is possible the pump picked something up and it clogged the injector.

well if it ran for two days then its something stupid like a blocked fuel filter on the bottom of the fuel pump caused by stale petrol ,which is what happens after a year of sitting

Check transmission fluid and filter.

I suggest you take it back to whoever did your transmission.

check for coolant in the oil, or oil in the coolant.
smoke is comming from somewhere, most likely burning coolant from blown head gasket. or rings are smoked and burning oil :( gunk on egr is probably burnt coolant. sorry for the bad news :(

if your air filter is blocked then the engine is choking resulting in lower revs check that 1st

Have he transmission drained and the screens cleaned

Don't think there's anything wrong with it. That's pretty normal for mine. If it's unusual behaviour for your car, check your coolant level. I almost ran mine dry last year and found in the days leading up to it that my idle revs were sitting around 2000 once the car heated up. If it turns out to be that I can give you some real handy tips for changing your coolant and flushing all the junk out. Much cheaper than a mechanic and good if you have a spare hour.