my truck still has rough shifting problems even after transmission repair? on 1993 Ford F-250

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my truck was experiencing transmission problems and rough shifting it is an automatic. had it so called repaired by a trans . shop and they told me it was electrical and that they dont repair that. I thought that when you have your trans. rebuilt that they also put upgrades in it and have to reprogram the "PCM" to the new upgrades and that entails correct shifting right ?????? this repair costed me $2800.00 and my truck is still broken. HELP!!
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Upgrades usually are special order. They maybe trying to say they either cant figure it out or dont want to warranty their work. I would get a second opinion. If you are told that it is something that falls into a trany rebuild job you or your lawyer need to go back there for a little talk. gl
thank you for replying...I have done extensive research and have also consulted another mechanic. and your right I'm afraid this mess is going to turn into a legal matter...Thank You.