STARTER/FLYWHEEL QUESTION

I can imagine only 4 ways for the disc to hit the flywheel bolts.
1)The bolt heads are too tall.
2)The flywheel has been resurfaced too thin
3)the front face of the disc is worn off, and
4) you are pushing the pedal too far down, and the fingers are pushing the disc back into flywheel,bending it and driving the hub into the bold heads.
Well I guess putting the disc in backwards could do it too. But that would create other issues .

You can align the BH with no dowels at all. The dowels are just there to make it repeatable so you don't have to dial it every time you take it off.Sometimes you have to "waller"(word credit to RRR) out the holes to make it fit. In your case I would check the faces for parallelism too. That is to say, that the block face is parallel to the tranny face.

If you have to push the BH over to the passenger side quite far, this will drag the starter drive into the flywheel, which might make it tend to stick. If it is also very noisy during cranking then you will have to move the starter away from the flywheel. This sounds easy, but will require some grinding and special installation instructions. It sounds to me like your crank not in the right spot. A rear main seal leak can be an indicator of that.It will be worn very oddly.Take a real good look at it. It may be very worn on the passenger side and hardly worn on the driver side. My 367 wears the rear seals this way but in a vertical direction. I have found no cure for this except to throw the block away. I've got too much into it to do that. I found that I could stuff a 383 rope seal in there and trim the ends to fit. I bought a 7qt pan and run it a qt and a half low.These changes made the leak more sufferable.But I know a certain machine shop that will never get a referral from me. It did not have this problem until they fixed it.