Somehow I must have missed this post before, so I have a few thoughts.
First off, I would have zero concerns about using a factory Ford cast crankshaft in an engine like this. I have been racing FEs since the 70s, and over the years, I have broke about everything in a FE, stock rods, split cylinder walls, split main webbing,even tore all the main webbing out of a 105 block, while using nitrous almost 35 years ago, broke everything valve train related,etc, but I have never had a factory crankshaft break. I ran the same 1U 428 crank in my low 10 second 428 for 14 years, (the crank outlasted 2 428 blocks), and it still magged good, my 427/454 ran high 9s with a stock 428 crank, and DalePs 427/454 ran 9.6s with a 428 Ford crank, and at a lot more RPM than I turn my stuff. Not to mention, these were in 4 speed drag cars, I typically dropped the clutch at 6000 RPM or more, never an issue.
Concerning the drilling of the oil plug behind the distributor, I have not done that in decades, and I have never had any issues with lack of oiling of the distributor or cam gear, or timing chain set.
REgarding the stock type pistons and TFS heads, I am still running the original "428 Super" cast pistons in the standard bore 428CJ in my 59. It is currently on the engine stand, and I am in the the process of installing my new TFS heads. I have mocked up the heads, checking for piston to valve clearance, and although the larger TFS intake valves are the tight spot, at least with the mild (.528" lift) solid flat tappet cam I have been running, both the soft spring and clay method, show there is no issue, .098" min. (The exhaust has tons of room).
As for factory rods, I have used stock rods for decades, never had any issues for many years, however, when I started racing FEs in the 70s, there were not many other choices, and I have made thousands of low 10 second 1/4 mile passes with LeMans and regular C7AE=B and CJ rods with better bolts, but back then, these rods were not 1/2 century old. I did have the occasional rod failure a couple of times, but now, unless I know that the rods history, I won`t use them in a performance built. My 427/454 had Crower rods, I had Eagles in my 331 SB Ford, and my current 347 SBF has Scat. That said, the 428 CJ in my 59 still has factory 13/32" CJ rods, I am using them, because it is a fairly low mileage engine, that had been sitting around my garage for over 30 years before I decided to freshen it up for the 59. That said, if I decide to rebuild this 428 again, or modify it , I have a new set of Scat rods that I will use. I just figured that for this budget build that will not see 6000 RPM, I will roll the dice.