Glad to hear it's cooperating with you now. I have to admit, I'm not really sure what connection the FR relay would have on the RTN circuit, but hey...sometimes mysterious things happen. I sat down with my E15 (an AA model) last night and found that my speed changes are reliably 1.5 seconds for 1st to 2nd, and 2nd to 3rd. The FW relay drops in a little faster, maybe around 1 second or a little less.
If you have the HSM, the schematic of the control card is on P5-24. The timing of the speed changes are controlled by the combination of the resistors (R109, R117, and R120) paired with the capacitors (C103, C104, C105). You mentioned the card was reconditioned, if the capacitors weren't replaced you should do that. If the caps were replaced, then you might consider replacing the resistors. If you want to go to a lower resistance value for R109 and R117, that would speed up the transitions. Maybe matching them to R120 would be a good thing (1.2 MOhm). Resistors can become more resistive over time (this is why the fuel meters read low over time), and may need to be replaced.
Good to hear you're feeling up to tinkering!