Jim;

Linked Pictures are not visible, please repost.

Overheating: If it did not overheat before work, and now it does, there's only one conclusion which can be drawn...something having to do with this work is causing it...first, verify Coolant level, and that system is burped of air...next is Tstat, because it is THE temp controlling device, and it has been changed, I'd look there next...it's proper function should be observable on the Temp Gauge, because Gauge is so fast-acting that the first opening should be apparent by a visible drop in indication (you can also detect Flow through Radiator after that by feeling temp of upper and lower hoses...before first opening those hoses will be cold) if you don't see the Temp drop first time it opens, remove Tstat, and test on stove, or just put back the old one. Buy cheap Tstats (without Bypass Pipe block-off), and you get what you pay for!

Shifting problem: Again, if it did not have an issue before work, and now does, recheck what was done. Symptoms still cause me to suspect Gearbox input shaft is not disengaging from Crankshaft enough...Clutch issue (is adjustment now?...linkage bushings OK now, no lost motion?)...or Pilot Bearing (which was changed) is somehow not allowing input shaft to turn with respect to Crankshaft. Is Shifter nut fully tightened on Gearbox lid?

Eric; Is there any way (without removing Gearbox) to verify if Gearbox input shaft is not completely free of Crankshaft when Clutch is (supposed to be) disengaged? Maybe starting it in Gear, with Clutch depressed, and Back Wheels off the ground to see it they get drive...?

Good Hunting!