Vacuum modulator is not recommended for a street vehicle. Stay with the EPC.
Not knowing the builder or his work, like I said earlier the harness or a ground may have been damaged. If not immediately after the accident, then maybe a wire was moved during repair into interference with something and over time the shielding got scuffed off creating a short circuit. Seen this quite a few times. Again, if you have or know someone with a Fluke 88 meter, check all the circuits for continuity.
If the 2-3 is the only thing that flairs, and everything else is good, then really the only build-related things are:
1) Seals around direct clutch apply piston are not sealing or the piston is cracked. Must tear down to inspect. I'll give the benefit of a doubt to the builder that he air-checked ALL the hydraulic circuits during reassembly. Believe it or not, many shops out there neglect this.
2) Direct clutch clearance set too high. Factory recommends .060" max... I set mine to no more than .030". On the factory setup, 0.080" or more can cause a flair on the 2-3. This can happen if you put in the narrow width steels (meant for the 9 and 10 friction packs, which I do not like due to the thin steels) in a factory 6-friction pack. You could try installing a corvette servo... the back side of the servo acts as the 2-3 accumulator... if the 3-4 clearance is a little loose the vette servo could tighten up the timing enough to overcome the flair. Not a permanent fix, but will work as long as you don't beat on it regularly.
3) Checkball capsule behind the servo leaks. It is common for many rebuild shops to neglect this check ball capsule. If it leaks, it will cause a 2-3 flair and will eventually burn up the direct clutch (aka 3-4 clutch). While you can see it in the servo bore (in the case housing) with both servos removed, the valvebody and separator plate must come down to replace this... an "easy out" bit makes a great tool for removing the capsule from the case. By hand, contact the capsule with the bit, turn until you feel it grab, then pull it out. Install the new capsule in the same orientation.
There may be a few things I'm forgetting right now. Transmissions can be hard to diagnose over the internet, especially if repeat rebuilds are occurring (which red flags to me the builder isn't experienced with the 4L60E).