H22A Transmission problems

I just had my engine replaced by my local garage, They swapped the H22A-1 for a J-Spec H22A 'Type S' along with the transmission that came with the engine. Now, the problem I am having is difficulty engauging gears and shifting out of gear. There seems to be a lag or hesitation while going into and out of gear. All gears. What could this be from? How can I fix it?? Are there any advised replacement tranny's for the H22A specifically that won't undermine my power?
I had the transmission ripped apart just the other day and the drive ring gears look good, the synchro gear looks decent, and other than some stupid comment about the transmission shift fork being mis-manufactured on preludes from cardomain.com I can't pin-point the problem. Has anyone else had the same problem?


And ps. there is no H22A-R.
Only: H22A, H22A-1, H22A-4, H22A S or also known as 'Type S'. And not all H22A-S's are JDM yo. JDM featured the H22A for a while.