Hey Brian and welcome,
I am sure others could answer your question about the programmer better then me and I am sure they will pop in here soon. From what I gather Bill should be able to make your trans do just about anything you want it to as long as the internals are good. This is were I think most your problem is. I would start by having it flushed. I have seen this fix so many "small" problems with transmissions. It could also be a valve sticking in the valve body or slipping clutches from being worn or low fluid pressure. Try the flush it could be an easy fix for about $150.
Hope this helps you some,
Chris
P.S. Just so you know I am an ASE certified master mechanic
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Chris
2001 F-350 crew cab 4X4
DIY napa air filter

4" turbo back exhaust
PHP flip chip--- stock,fuel sipper, 100hp, 140hp