What bellhousing and trans vintages are you using? On my 59 Ford 2 door sedan, I have a 428 Cobra Jet engine, a 1966 small block wide ratio Toploader, and a 1961 cast iron bellhousing. The early (pre 65) Ford manual transmissions use a smaller bore size for the transmission front bearing retainer than later models, so I had 2 options. I could either find a 1964 only Toploader bearing retainer, have the larger retainers OD machined down to the earlier size, or do as I did, and have a machinest bore the early bellhousing to the later size (4.84").
Concerning the small block vs FE input shaft length, yes, the small block input does have a slightly longer pilot tip, but on my car, I mocked up the engine/trans/bellhousing without a clutch or flywheel, but with a pilot bushing, and, at least with my setup, the small block input had enough space to allow the trans to go all the way in, and still have sufficent space between the pilot bushing and the splined section of the input shaft without needing to trim the tip of the input shaft. Like Larry said, a old steel input shaft fits much better than a cheap plastic line up tool , if the input shaft slips in and out of the clutch when its all bolted together, the disc is centered, and there should be no need to loosen the pressure plate bolts, or depress the clutch pedal to make it all fit. Like others, I have had the odd occasion where the trans didn`t want to go in properly, walking away for a bit, then retrying the install with a fresh attitude, usually does the trick. before installing the clutch assembly, did you test fit the disc onto the input shaft, to confirm the disc slid easily onto the inputs splines? Check that the new throwout bearing easily slides all the way along the bearing retainers sleeve? That the pilot bushing fit properly over the tip of the input? Often, even if your attempt to install the transmission has the input tilted just a little bit can prevent an easy install.