Transmission issue

[spitfiremk4]

I have been experiencing an intermittent tranny issue ever since I had the IMS bearing upgraded/replaced.
Once in a while it is like all the upper gears are missing ( R,1,3,5 ) and the only way to get it back is to put the car into 2nd gear.
I have taken it back to the mechanic that did the bearing, which obviously involved removing the transmission and he looked at linkage connections at transmission and said it must be the tranny itself.
This NEVER happened prior to repair, is there and cable issues or bushings that should be looked at or replaced?

Thanks,
Karl