Im studding the mains and wonder should i just run the bolt under the oil pump or remove the washer and whittle down the 12point nut and notch the pump. Any help? What do you guys do?

I cut and chamfer the stud, and spot face ( mill) the pump stud boss area down on the pump housing.

i just ran the regular bolt for that cap

I cut the stud down, ground down the 12 pt nut and the pump for clearance with no washer.

I milled the spotface on the main cap down, and cut some off the stud so I could use the standard 6 point nut and washer.

I did it the same as FlyFish, but I think Dartman366 has the best approach and it's what I would do the next time. About .100 spot facing should do it. Some grinding of the pump housing will probably still be needed.

maybe like this??

If you mill the cap, use an end mill with a radiused edge otherwise the cap can break at the corner of the mill mark. I've done it both ways. I cut the stud and ran no washer on my own motor but I've milled .120" off the cap on every motor that's come out of the shop I work at.

Or... you could run the bolt.