To answer the thread title question... both. Do the J-mod if you want to try to get as much out of the remaining life in the 94 trans, and get a tune to take advantage of the mechanical changes.
A couple things here related to your situation. First, the computer - if the correct speedometer gear was installed to adjust for the change in rear gear ratio - can compensate for the change in gearing. Technically, up to a 20% change either direction from stock can be compensated for; if the car came with a 3.27 stock, you're fine in that regard. If however, the car came with a 3.08, you will need a tune. The car would consistently shift at a relatively 'low' vehicle speed or RPM. Around town shift points are primarily controlled by throttle/pedal position vs. vehicle speed.
The J-mod is used in conjunction with gear changes because it reduces the clutch fill times and thus the time it takes between when a shift is commanded and when a shift is completed. Because a shorter gear causes the RPM to rise at a higher rate and the PCM commands the shift at the same RPM, you might hit the rev limiter because the shift 'takes more RPM' to complete. Doing the J-mod to reduce shift completion times brings the RPM change back down.
Now - as for your situation... a leaking 1-2 accumulator o-ring seal will cause a late 1-2 shift, no 1-2 shift, and/or a shudder on the 1-2 shift. On the other hand, a failing intermediate one-way clutch will cause a late 1-2 shift that finishes with a 'bang'.
That said... to me it sounds like a more likely to be the one way clutch than the accumulator, but then again, I'm not riding in the car with you when it happens.
If you plan on keeping the car for any length of time, money would be best spent on a 99+ transmission swap.