I just pulled the 428 CJ out of my 59, which I have been running for almost 1 1/2 years now, a bit over 3000 miles. I have a Toploader 4 speed that was originally from a 1966 Fairlane with a 289, using a bellhousing from a 1961 Ford car, and the later style 184 tooth flywheel and starter. I know that some guys say that the longer tip of the SB input shaft would bottom out in the crankshaft, and the tip needed to be cut down, or a deeper bellhousing from a PU truck would be needed. At first I did try a C5T truck bellhousing, but that located the clutch fork about 1 1/2" lower than the car bellhousing, causing problems with the factory clutch linkage, so I went with the 61 car bell. Now, when I was first doing this, I did a rough measurement, and found that the SB trans would fit just fine with no modifications, so I put it all together. Now, 3000 miles later, I pulled the engine and trans, as I have a cylinder head issue, as well as need to upgrade my clutch. Anyhow, since I have everything out, I decided to check over the pilot bushing, trans input, and crankshaft hole to just see how much room there really is. What I found is, that from the back of the pilot bushing, to the bottom of the crank hole, is 1.49", at the center, and 1.37" at the outside edges of the hole. On the SB Toploader input shaft, the tip is 1.14" from the end of the tip to the beginning of the splines, which means, that even if the splines were to actually be touching the pilot bushing,(which they do not), there is still about 1/4" of space between the tip of the input and the bottom of the pilot bushing hole. I also measured the mark on my SB input shaft to see how far into the pilot bushing the tip actually went inside, in my case, it was .096", so in reality, I had over .400" of room between the tip and the bottom of the crankshaft hole. Now, it is probably still best to check there measurements on your own combination, but in my case, the pilot hole in my 1UB 428CJ crank has plenty of room to accept a small block input shaft without trimming the tip down, using an early FE (narrow pattern) car bellhousing. Your results may vary.
Oh, by the way, much like the discussion about the input shaft tips, the flat tappet cam and lifter " fiasco" is also not written in stone either. I inspected each of my plain old dumb bell flat tappet lifters (no fancy coatings, drilled oil feed holes, pre-broke in on a machine etc), and they all still look like brand new. So, it seems that not every new flat tappet cam "goes away" during or shortly after break in, if the correct steps are taken. This engine was assembled 5 or 6 years ago, broke in on an engine dyno, and then sat for a few years until I finally got my 59 on the road in the summer on 2020, and drove it over 3000 miles.