belive it or not, shift uncertainty could easilly be attributed to a weak injector... hear me out.
if the injector is not working to spec, your other cyllinders will be working to take up the load. so you will put your foot into the pedal a bit more, and the tranny shifts based on where your foot is.
it certainly will not hurt to change gaskets, fluid and filters, and I really like synthetic tranny fluid. but getting the engine running solid may solve your particular problem. the surging kinda makes me think engine problems, possibly timing chain, or valves.
I am not a Diesel Mechanic, but my 82 SD runns like a sewing machine.
John