I have an Eastman 864 F tuba (great tuba, by the way), but the 3rd slide is too long.... 5th position (2+3) is always flat

I'll take your word for this...
Typically (with many conical brass instruments) the 2-3 combination (just as with 5th position on a trombone) is severely sharp for some pitches and severely flat for others. I'm pretty sure this is because there's a tremendous amount of cylindrical tubing involved (distorting the taper) YET it's used for FOUR pitches - rather than only two, such as with 6th and seventh position (or 4th valve and 2&4 valves).
Typically (valve combination 2-3 with F tuba) 2nd partial C# (just below the staff - F tuba) tends sharp, 3rd partial (G# at the bottom of the staff - F tuba) tends slightly sharp, and C# (middle of the staff - F tuba) tends flat. whereas the top C# (just above the staff (also tends flat.
BUT THESE CAN ALL VARY ON VARIOUS MODELS OF F, E-flat, C, and B-flat TUBAS (as their body tapers all vary from each other so drastically)...
but (in general, being less specific about particular partials' tuning characteristics) 2-3 is "squirrely" (again, just as is 5th position on the trombone).
Eastman rotor tubas are (sort of, though some config and taper differences) copies of early B&S F tubas.
With my (6-valve) B&S F tuba, I LOWER the pitch of the C# below the staff by playing it with 1-2-6, whereby I can tune the #3 slide to FAVOR the two flat-tendency pitches played with 2-3. G# (as far a so-called "slot") is so barn-door wide, that I can put it anywhere (as long as I'm paying attention - and I believe I generally do).