I think you are doing the right thing. I find removing the old dowel pins, dialing it in, bolting it tight and then reaming the holes out and installing oversize dowels the easy way and this is what is recommended in the old factory maintenance manuals recommend and its still done today on Cummins Diesels. However, if your machine shop is more familiar with offset dowels, that's fine too. Again, I think you are making the right decision to correct it. Your clutch will work smoother and proper alignment relieves a lot of strain off the input shaft bearing and the entire front of the transmission. If you are looking for low end torque, you will have it in the SM420. It would climb trees if you could get traction.