Never done a 4" stroke, but I've done two 4.100" strokes...one on a production block and one on a new Dart block. The production block only needed the cylinder skirts notched a tiny bit (I'm very surprised that you had to grind the cylinders on a 408). The Dart block didn't require anything.
I'm curious to find out what you used for an
oil pump pickup as I've never had any problems with clearance whatsoever, except for having to tweak one to get the pickup/pan clearance set correctly.
If you're used to Chebby's, you're in for a treat when you build a Ford engine....no pencil sized main fasteners, no cam buttons for roller cams, and no extreme grinding. I just finished a 383 for a buddy and had to grind on everything, including the ends of the rods where they touched the cam.
One thing for the next time you do a 408, use the forged I-beam rods. You probably won't have to touch anything at all. I use I-beam rods extensively now. They are plenty strong enough, they are lighter than the H-beams, and they're a lot cheaper than the H-beams. You can get a set of Scat 4340 I-beam rods with ARP 7/16" fasteners in a SBC length (for SBF strokers) for about $250-275.
Instead of a heavy assembly lube on the cylinders, I usually just *lightly* spray my ring compressor (tapered) with WD-40 and *lightly* wipe down the cylinder with WD as well. This will help the rings get a good bite right off the bat.
Be sure and let us know what she makes with those cylinder heads.