To fit the rear main seal is really easy, but you need to do it with caution. You'll be removing materiel from the seal. If you go too far, you can't put it back on and then you'll need a new seal.
The issue is every time you line bore or line hone the mains, you make any hole in that line smaller. That includes the main seal groove. It has to get smaller to. That is what happens when you cut the main caps. You make the main bearing bore smaller, and then you hone it back to round and to size.
The issue is you don't go back and open up the seal bore. I suppose you could, but you'd need the blueprints from the factory to see the size and tolerance AND you'd need to use a boring bar AND have the correct tool to open the main seal groove up.
This is why so many guys have a good loathe for split main seals. A one piece seal eliminates this issue.
Clean the main seal groove in the cap and block. Slip the seal into the block and measure how far the seal is proud from the block. You don't need much more that .005-.008 proud. If you have more than that, you need to very carefully use a belt sander (I just use a bench mounted belt sander) and carefully sand off a small amount from each end. Go slow, and take small bits. Clean the seal every time you sand it. Slip the seal back in the block and measure again.
Again, I can't emphasize taking your time. If you sand and measure 10 times...sneak up on it. Once you get down to .005-.008 clean it up and do the same thing to the cap seal.
Now you can put the seal in the cap and the block and not do all that kookie crap about clocking the seal so the mating surfaces of the seal don't meet at the parting line. That's a bad deal. The seal is designed to be crushed at the block/cap interface. Changing the clocking effectively changes the crush, but the seal will still be out of round and leak.
I used and brand new, never touched X block on my engine and I had to fix the seal. It was .020 or some crazy amount proud. I did have to line hone it a bit to get everything round and straight but that was a bunch considering it was a new block.
That's the way to fit a main seal. If you picture in your mind what happens when the seal has too much crush (the seal is too proud out of the block) you'll see that as you over crush the seal it goes out of round. It may seal for a while, but since it's not round, you will get local hot spots and the seal won't be correctly loaded against the crank. This wears the seal very quickly and the leak comes right back.
Same thing with a main or Rod bearing. They have the amount of crush the designer wants built into the bearing. So the shells are proud of the block. Make the bores too small and you will squeeze the bearing out of round. Make the bore too big and the bearing won't have enough contact load against the bore and will overheat. And will spin in the bore.
Fix the crush issue and I think you problem will go away.
Please keep the forum updated, as this comes up all the time.