First I'd have to ask why the clutch was changed. Because it was slipping, or, acted similar to how it is now. If it acted similar, and it's still doing it, I'd have to suspect part of the linkage mechanism is worn. Quite possibly where the yoke attaches to the cross shaft. I'm not familiar with the A-C set up, as I'man IH guy, but most have a woodruff key, between the yoke,and shaft, and clamped in place with bolts. If a PO has gotten a little over zealous depressing the clutch pedal, could be the key is partailly sheared, and your not getting a full throw on the yoke.
Second, how was the tractor reassembled..?? Was it jiggled back together, until the splines engaged, and meshed, then chase the bolts up to hold it in place..?? Or, just drawn together with bolts..?? Did an stub shaft alignment tool some in the kit..?? Using Google images, I'm seeing the flywheel is similar to an automotive flywheel, where an alignment tool should get you pretty close. At this point, the driveshaft should at least get started through the clutch plate, until it comes to the splines matching. At this point, I engage the pto, and take an adjusteble wrench, and turn the pto shaft. When the splines match, you can feel them mate up. If it binds up here, and doesn't want to go, and too much pressure was applied with bolts to draw it in, there is a possibility the center metal plate was bent/warped. Same thing when it reaches the pilot bushing. If the center plate was sprung, it could cause some drag in spots between the face of the clutch plate, and flywheel.
Anytime I feel any resistance when going back together on any I'm reassembling, I'll take an adjustable wrench, and put it on the clutch release lever where the clutch rod attaches, just enough to relieve pressure on the clutch disc, to let it align. This will happen at 2 spots, when you get to the clutch disc, and then again at the pilot bushing.
I also use 2, to 4 long bolts threaded in about the center holes on the clutch housing, and block, that are basically guide pins. I'll engage the pto, and put the tractor in first gear, then use a wrench that will fit over the pto shaft, and turn it to move the tractor ahead, until I can "feel" the splines try to mate. At this point, I get on ususlly the right rear tire, and turn it forward, jiggling it ahead, then follow up with bolts, just enough to hold it in place. All the while, checking to make sure the space between the top of the block, and clutch housing are pretty well even spaced. If not adjust one end or the other accordingly.
All that just to say if things weren't aligned pretty close, and it was drawn together with bolts, forcing it, it could have sprung the clutch disc. I'm sure the machine shop that refaced the flywheel, also cut the surface where the pressure plate attaches, milled it to specs to match the .030. Even if they didn't that should cause slippage problems, not dragging. But doubt .030 would make that much difference on releasing.
Without knowing the specifics of what was checked for wear, or how it went back together, it's tough to diagnose. I'd have to say your best bet is to split it again, and see what the problem is.