We had a similiar clutch setup in our stock pulling tractor. "Truing up" the 3 pin driver isn't really needed, if it is warped that bad it should be replaced. Check the bushing inside the driver hub for wear. 3 pin or 6 pin driver? The six pin is used in pulling to spread the stress of the driver to 6 holes on the clutch disc instead of 3. This isn't needed for non-pulling applications. If you use the cultivator spring, make sure to install the inner liner inside the spring and over the drive shaft. We never had any trouble with removing the teaser spring and cup and running the lock washer with a spacer. Roll pins or studs? If the roll pins are in good shape, leave as is. If you decide to go with the six pin set-up, the threaded studs will have to be installed or the extra holes would need built up like the original three so the pins won't pull out. Aluminum clutch disc? It does not slip. Good for pulling, but a pain in the butt if you are wanting to slip the clutch to back up or pull forward. A lot of guys are running the Kevlar discs that either Midwest Super Cub or Vogel sells. 3" or stock coupler? I don't understand the stock coupler being drilled offset. We use bolts in 3" coupler in our puller. We get some that has a long un-threaded body that keeps the threads out of contact with either the coupler, drive shaft or pinion shaft. We run the 3" coupler to be able to change over the pinions set while in the tractor. Running the clutch assembly at 3800 rpms will probably not cause too many out of balance issues.
Good luck with your project.