This is not uncommon. It will need a little "clearancing" aka whack it a few times with a rubbler mallet. I had a similar issue a while back. Assembled an engine with the RJC pan and when I got it in the car and started it it made all kinds of racket. Took me a while to figure out the #5 and #6 rod cap bolts were just barely hitting the windage tray at the bottom of their stroke. You couldn't hear it when rotating the engine by hand but the scrape marks in the tray were the giveaway. Couple of whacks with a mallet and all is good.
I was actually talking about the pan rail interfering with the main bearing cap studs, but you bring up a good point. Since the motor is a stroker, I will probably have to 'clearance' the windage tray also..
Anyone else? Any other oil pan options?
I'll assume you're talking about the #4 cap, and the nuts are hitting the pan rail? Either switch the 6-point nut to a 12-point, or spot-face the cap down for clearance.