Ideally, distance scales will be pretty close to actual. BUT they are luxury items. Like cup holders in a car- handy but not necessary to drive a car.
You have probably the most important thing down- getting the taking lens/film plane image match focus with the viewfinder image. With that in place. all the rest is gravy, except maybe getting to infinity.
I have no idea what you mean when you say that you 'took apart the camera.' That could be ominous, or it could be you did what was needed to adjust focus and nothing more.
I'll describe the 'standard' way to adjust TLR focus. This assumes that you have the camera disassembled in the following way- 1), the cover on the focus knob is off and the screw holding the knob in place can be loosened; 2) the lens shroud covering the viewing lens lock screw is removed. That's what you need- access to the knob lock screw and access to the viewing lens lock screw. Nothing more.
1) Have something in film plane, like your grease paper. Lock shutter open, open aperture.
2) Focus taking lens on INFINITY- distant object, collimator, another camera set up fro this (search rick oleson collimator hack)
3) Adjust focus knob so that it is at infinity stop when the lens has infinity object in focus.
4) Using same infinity target and with focus knob set to infinity, adjust viewing lens so that it is also focused at infinity on the focus screen. Lock it down.
Done.
Again, getting the focus screen and taking lens to agree is the key issue.
Not being able to turn the focus knob to infinity is concerning. At the least, if infinity is out of the question, I would use a target 10/20/30 feet away, not 5.