Could be the fluid causing the shifting difficulty....mine hated Pennzoil Synchromesh and Royal Purple Synchromax, both made shifting sticky and notchy, and created shifting oddities between certain gears. Synchromax cause such bad shifting characteristics that I had to force the shifts in and out of the gates between gear changes and double clutch...one fill, and it was so bad in 500 miles I thought it damaged the transmission.
I ran a blend of Redline MT-90 (one quart) and MTL (remainder of fill) with very good luck...I also ran fast coolers for the added volume. I determined that my particular 5600 preferred a slightly more viscous oil: Redline MTL was the thickest, the PZ synchromesh was middle of the road, and RP Synchromax was the thinnest...adding a quart of MT-90 bumped the viscosity up just a tad more and made my particular 5600 shift as nice as I could get it to...it would never feel like a car, it still is a medium duty truck transmission.
I put 297k on that rig, redline for the majority of those miles...