It's been a week, so I'll bump this one in case anyone didn't notice the edits.
Here is how the ElectricMan and ProtoBluesMan battles will go if I can get the special wood chips I need from the trader quickly enough.
http://dehacked.2y.net/microstorage.php/info/836540330/ElecProN.vbm
The Snakegg1 + WoodTowr strategy does save some time, at the expense of a trip to Higsby's sometime before the SciLab party. I think the fastest time to visit is just before opening the car with the kidnapped boy. Since we'll want to dump the rest of the chips into the trader the same way later on, it won't be a loss as long as it doesn't take more than a couple of seconds to manipulate the right chips to come out amidst the new chips.
Another thing I looked at just now is that first battle against ElecMan. I was thinking it was faster to grab a random ShokWave P next to the merchant in Internet-3 than to run over to the ShokWave L at the beginning of the school network, so I came up with another strategy for the unbeatable ElecMan that's just as fast: Two Cannons followed by a TriArrow. Yes it does require two extra shots per Cannon to reach 50, but ElecMan's healing is on a kind of "frame rule", where as long as he doesn't get a chance to move and doesn't get stunned by the attack, he'll heal at the same times.
Since I couldn't figure out the ProtoMan glitch, I moved on to the boss fight at the end of Area 4.
http://dehacked.2y.net/microstorage.php/info/1838286043/Bluies.vbm I suppose the only way to be faster would be to hit the other HardHead the first time it opens, but I can't get the chips to start up soon enough for that.
Here's a BombMan battle fought with FireSwrd and GtsShoot that requires perfect luck.
http://dehacked.2y.net/microstorage.php/info/1445814407/BomberfG.vbm HiCannon would only help if the bomb only did 210 dmg instead of 280. FireSwrd G is easy to get from the trader, but it requires the bombs to be in certain positions in order to be able to set off the chain reaction, which requires more luck manipulation. Heater and RedWave have better range, but RedWave doesn't come in G code, and Heater G can only be won from a random battle. So even with the extra bit of luck manipulation, the FireSword strategy should save a second and a half over the complicated two-turn strategy. But it also means that the fifth PowerUp is useless, and the HiCannon and TriSpear might not quite pay for themselves... Ah, we'll see.
If I do have HiCannon, then the MagicMan battle can go like this:
http://dehacked.2y.net/microstorage.php/info/681454404/MagiThun.vbm It turns out that ThunderBall3 is just as fast as TripleSpear in that battle, so if I can pick up Thunder3 G from the trader without delay, then... that makes TriSpear only useful on ColorMan. Now I had been thinking of TriSpear, Recov200, and 3000 zenny as a package deal in jacking into the Waterworks control panel, as if I cut out the TriSpear for not saving enough time, then the other two probably aren't worth the jack-in time either. Cutting all three will make the chip and money budgeting even trickier to work out to find the fastest way. Getting six particular chips from the trader may be tough to work out, too, as now I'm planning on Snakegg1 N, WoodTowr N, DynaWave C, Quake3 C, FireSwrd G, and Thunder3 G. What do you think?
