If it was a linkage problem, it wouldn't be temperature dependant.
Did it shift like this before the "rebuild"?
To me, it seems more a question of what fluid the transmisison was filled with.
It is normal for cold shifts to be "stiff", but not the extent you describe. If possible, find out what the trans was filled with. Better yet, take it back to the the shop that did the work and ask them to drain and refill with Redline MTL.
My 2.3345 cents. I'm sure others will chime in.
uberhahn
'94 530i 5-speed. The work begins...