If you don't want to use the spacer/adapter, you use the early model input shaft length. I have a home grown modified 3550 on a Lakewood bell, with a spec 3+ in my F100. I originally had to use a spacer as well because the late model input shaft was longer than the top loader stuff, apparently. This was back when the 3550 was the only "street oriented" upgrade stick shift fox mustangs had available, so the dimensions seemed to tailor to that crowd with no other available options. I did this conversion roughly 20 years ago, on a truck I was still 2 years too young to drive yet.. so I don't remember exact measurement differences etc. I will say, that my Lakewood was concentric right out of the box when checked with a dial, and I used ARP bolts for clutch and flywheel (centerforce billet), right out of the summit catalog. Never had a single problem with any of the above. Used blue Loctite and a torque wrench to install, like a good little boy. That centerforce clutch was pure garbage though. I've since seen pencil sharpeners that would probably overwhelm that thing... Pilot bearing came from local parts house, although I prefer a bushing over a bearing these days. Seems to shift a little better - go figure - they had it right the first time.
I upgraded to 26 spline input this last time, and got the top loader/early model length input so I could get rid of the spacer. I did this both for input strength, and to cheat my shifter away from the bench seat a hair. I.E. - you could go either route without giving up anything, but you may want to consider where either/or lands your shifter.