Whipple104 is the 722.6 expert around here, but here's what I know. Get a later trans and put the 104 bellhousing on it. There was an upgrade around 01,or 02 that keeps K2 from exploding. There are two different sets of gear ratios depending on if it was from behind a 4 / 6 compared to an 8 / 12. Stock management will not tolerate mixing and matching planetaries between the two versions. There is an extra beefy version from behind the ttV12 and 113K but its likely overkill unless you're close to 1000hp. IIRC, Whipple104 pushes somewhere between 400-500hp though bone stock 4cyl versions without issue. I built a beefy 722.6 for my coupe and stuffed it full of clutches. The biggest thing I accomplished doing it was making it difficult to tune for smooth shifts, especially the 1-2. On the up side I wouldn't be able to break it with triple the HP I currently have.

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90 300TE 4-M
Turbo 103, T3/T04E 50 trim
T04B cover .60 AR
Stage 3 turbine .63 AR
A2W I/C, 40 LB/HR
MS2E, 60-2 Direct Coil Control
3" Exh, AEM W/B O2
Underdrive Alt. and P/S Pulleys,
Vented Rear Discs, .034 Booster.
3.07 diffs 1st Gear Start

90 300CE 104.980
Milled & ported head, 10.3:1 compression
197° intake cam w/20° advancer
Tuned CIS ECU
4° ignition advance
PCS TCM2000, built 722.6
600W networked suction fan
Sportline sway bars
V8 rear subframe, Quaife ATB 3.06 diff