Ok. time for some scolding, some praise, and then as much advice as I can provide.
Scold: no!!!!!!! stick with Starfox 64 and Sin and Punishment!
This game I found will be really frustrating... it desynchs (since it is one of the 4 N64 games that heavily relies on the Exp Pak in order to include the BW campaigns), and will require many many many many many many many rerecords in order to find the optimal time to end a mission with one final attack.
Also, before recording remember to delete the .fla file in the mupen save file directroy before recording, then whenever attempting to watch from the very beginning, delete the file before watching. this will minimize non-exp pak desynchs.
Praise: This would look sooooo cool if done. (but will require a lot of motivation, dedication, and time/effort.)
A full run would be all 6 campaigns. I think that, at the moment, due to the difficulties and that we don't know how long it will take to do all 6, we should only do one, and see what happens. You can do any campaign in any order, and based on my initial problems with it and lots of thinking/planning, concluded that BW Zerg and BW Terran would be the best campaigns to TAS first. (if you're going to end up doing them in order, then do them in order- I don't recommend it- but individually, BWTerran and BWZerg are the best, trust me. either one.)
I love your work, and know full well that you're a starcraft fan/player, so I know you'd do a wonderful job on this.
Advice:
I'd say do whatever you want mode. BW Zerg or BW Terran.
Once you get to the very first mission, pause the game, go to options, and increase the speed to max.
Go to SDA; they have PC speedruns of every single mission. (they are incredibly fun to watch as well. if you are going to do this, I might just redownload the campaign you're doing.)
Linkie for Vanilla Campaigns
Linkie for Brood war campaigns
read through this entire thread. there is an improvements route by Flagitious of how to improve the SDA times, as well as one discovered strat that saves minutes on some Terran mission, I forget which one.
Also within this thread is a list of all the command shortcuts, most of which will be very useful. Such as quickly selecting a building to make, selecting certain types of units, making a map "savestate" with the D-Pad that you can use to monitor different bases/attack zones (very helpful). make sure you know them all.
and finally, I have a
Link to the most comprehensive Starcraft site ever. This has complete advanced/basic strats, has many members who'd love to become a mentor/guru or give information, and lots of other goodies.
"It will be done!"
Good luck!