I keep in pretty regular contact with Scott. He definitely has to rotate the knuckles [I seem to recall something like 6-7 degrees] even with the dual cases. His pinion angle was pretty good with his planned CV driveshaft, but his caster was too negative.
As you probably already know, he is running front shackles, so your application may be slightly different. With your spring angle, the caster might be OK, but the pinion angle might be a little low with a CV driveshaft; if you use a regular driveshaft, you might get lucky.
3 Franklins for a pair of gear cases with the adapter sounds like a good deal; heck, the adapter alone is that much new. You may want to check with Marlin about what is involved with the adapter [?simply swapping out the sleeve] if you go to 23-spline. Just curious, do you have an auto or a manual; if an auto, 2.28/2.28 is probably just fine?
As far as "needing" to upgrade from 21-spline, I have been running my gear case for right at 20 years, and have only broken one input shaft. Bear in mind that for 18 of those years, I have had a 4.3/T-350 in front of it. I broke the shaft when shifting from reverse to drive while rolling backwards down a hill with 38's, so they are pretty tough.
I just recently put 4.7's in, since I don't have enough wheelbase to do dual cases very easily. I stuck with 21-spline since I didn't want to have to change the output shaft in my tranny. Marlin's gears are definitely much beefier than the factory input shaft, particularly in the critical area where I snapped mine.
'10 RAV4 - 3.5L [269 HP], active 4WD, Sport suspension - really fun car to drive
'02 Tundra - 4.7L, 4.30 diffs, Kings front, rear AAL and anti-sway
'xx Toyo-Heep - 4.3L TBI, TH-350, 4.70 xfer twin stick, 4.10 Detroits F&R in 8" Toyo diffs w/4-wheel disc brakes, Champion beadlocked 35" BFGs