Dondragmer has put together a new tutorial that explains this process. It's exquisitely detailed with pictures and step-by-step instructions along the way. And check out his amazing kill score below! If you've got the GOG version of WC1 for the Mac, be sure to check this out and get credit for all your accomplishments!
For most classic games I have a DOSBox installation with a C: drive full of games, and I adjust cycles as needed. However, GoG provides a nice graphical front end, so I thought I'd try playing through WC1 using that.
I got to the end of the Vega Sector campaign, but at first had trouble finding my saves. If you can't find them either, read on. If you aren't using Mac OS, or aren't using the GoG-installed version of WC1, this entire post will be irrelevant.
What we're delving into here is actually the Boxer front end for DOSBox, which GoG uses for their Mac OS versions. If you need to look inside some other DOS game, the same principles probably apply.
Here Be Dragons
We're about to poke around inside your "Wing Commander 1.app" application resources. Mac OS does not make this easy, because you can corrupt the application this way. Look around, but don't modify files without understanding what they're for.
DOSBox used to default to 3,000 cycles. The GoG version of Wing Commander 1 is pre-configured for 4,000 cycles. I found this unplayable, and slowed it back to 3,000 in "DOSBox Preferences.conf". Considering what this does to the game, you would be justified in saying that these scores were "tool-assisted" in the way that a tool-assisted speedrun is.
I see there's some discussion of maximum medals achievable. I did intentionally fail missions in order to do Brimstone and Rostov, but I didn't leave aces alive in order to game that system. However, a cursory search hasn't shown maximum kills - apologies if I missed it. While I scored 695 (not including final missions where you can't save or see the chalkboard), you definitely face over 700 ships by the end of SM2. Apart from the odd ship that got by or was destroyed by allies, I bypassed the final 5 Jalthi in Corsair System Beta Wing because I simply could not keep enough afterburner fuel after the earlier encounters in that mission.