They are still telling me it has an aliginment problem which by now I have found a factory work shop manual which tells you how to go about aligining the trans to the engine.
You said this shop rebuilt your trans. Are you certain you got back the original trans (if they do alot of trans it is possible they gave you a rebuilt but not neccesarily the one you brought them, it is possible) / OR is this a transmission you sourced from else where {salvage yard, other car you owned, buddy}? Is this the original trans to this engine. If it isn't, then there could be alignment issues, you should have checked that when swapping (if thats the case).
You have answered your own question, you just havn't realized you have the answer.
If the shop your using dosn't know how to align the trans input shaft centerline to the crank centerline, then find a different shop or do it yourself. (If your capable).
Follow your service manuals (which book do you have, btw, please?) instructions for aligning (and any other repairs/inspections for trans) and you should solve your problem.