There were three assault shotguns, a plasma shotgun, phaseshift boots, gothic armor, BFG 10K, laser rifle and a hell staff (which I didnt bother picking up.) I entered the vaults with three phases, four large medpacks and a few stacks of ammo.
Sounds like you had a lot of ammo issues in general. It's not ENTIRELY surprising, playing on ITYTD like that, but keeping a good five/six stacks of plasma in reserve should not only be possible, but keep you going until you hit an Arach cave, or Spider's Lair, or commandos/arachs in a level, or just some plasma lying around (which, if I recall correctly, is doubled on ITTYD). When possible, kill stacks of non-plasma enemies with rockets: keeps the plasma fresh for important battles.
It's a damn shame, too, because you had so many plasma-based weapons. A tip (in case you wanted to kill Cybie): unload all your other weapons for the sake of ammo on your primary. BFG 10K probably would have been the way to go in such a situation, although you have to be close enough (and open-spaced enough) for the shots to count.
'm surprised you didn't get the Hell Staff, that item is like a godsend for Vaults. It would've turned those three phase devices and four med-packs into seven phase devices, basically. Although, you were lucky enough to hit the center on the first try, so...it worked out.
Made it to Captain at long last :) Now I can work on those platinums.
I don't mean to be rude, but I'm wondering which golds you picked up. Looking at what's available, I realize that it's entirely possible to hit Captain without increasing your difficulty to UV (or, technically, HMP, but I know you play on that). Platinum badges, with the exception of Quartermaster, are entirely UV/N!-based (with the UV ones being particularly nasty, like Conqueror). Unless you have decent number of UV victories under your belt, I might hold off on going for the Plats. UV is a big step up, and N! is an entirely different way to play the game (and, in most regards, harder than even UV).
I only ask because I haven't seen a UV YAVP from you on the forums, so I'm just making sure you know what lies ahead.