Re: 406 oil pan
I ran the I beam rods due to the reduced weight so I can't answer that clearance question. It is riskier, but the I beams are really lightweight for the price.
I did have clearance problems with my oil pan/windage tray/oil pan studs. It was a really tight fit with the Diamond Stripper on the inside. I ran a stud kit for the pan bolts and the nuts are super hard to get on. I had to heat and massage the areas around the studs to get the nuts on square.