Boosted Reflexes and Synaptic Accelerator started getting stacked as soon as Synaptic Accelerator came out in Cybertechnology; hell, that was one of the tricks I used when I made my first biosamurai. The theory was simply this: Boosted Reflexes enhanced the chemical makeup of your nervous system (from fluff, Street Samurai Sourcebook, 1e). Synaptic Accelerator enhanced the neurocellular portion of your nervous system (from fluff, Cybertechnology, 2e). Therefore, functioning upon two different-but-complementary portions, they would stack.
The only thing that might have stacked with Move-By-Wire (now with TLE-x!) would have been ... I forget the actual in-game name for them. The reaction enhancers, the levels 1-6 ones that were added to your spinal column and basically sped everything up, added +1/level to your Reaction (and thus initiative). I can see both sides of the the argument on that one, but would have come down on 'no, MbW is nasty enough'.