First off I want to apologize in advance for my mood, I just got off my 8th 5 hour flight in the last 2 weeks and am sitting in a terminal with poor amenitites for the digital traveler. Stupid layovers. I would also like to preface my tantrum by once again asserting that I was really only musing about the story that surely exists, even if only in fantasy.
Kelsier would not have had much if any trace metals. You get trace metals from what you would ingest and being a prisoner he probably didn't even have access to metal utensils, more likely a stick and a flat stone or a community trough. We know he would not have a store of metal because either you burn the metals, expunge the metals through the digestive tract or you get sick. If it were just metal anywhere in your body, Allomancers would have earrings galore or metal balls embedded in their skin. So either he stumbled upon some metals, ate some rocks which might not even have one of the base metals or used what little trace metals he may have had in his stomach at the time which undoubtedly would not have lasted long at all.
Kelsier might not have had access to atium at all. It was hard to come by, considering that he got one from Mare because he had not found one. While there are valid explanations as to how he acquired atium, they would all be a little too convenient. If he took from another worker, you would wonder how the worker found one so soon after having to turn in their atium to live another week. If he stole it from storage, you would wonder why it was so easy to get; prisoners would just steal a couple and turn those in if they didn't find more. If he just dug up another in the pits, you would wonder why he went the whole week without finding one and then got one from Mare.
Even if he was able to find atium and the other metals, he was not prepared to use them and would most likely flared and burned them up in the first fight he came across. He didn't have years to train like Vin, he had hours.
If it were as easy as killing each guard one after another, why then would he not have escaped much earlier with Mare still alive? They left Mare alive when they put her in despite the fact that they knew she was an allomancer. They assumed she was only a Tineye, but she could have easily been a Mistborn too. The pits were more prison than mine, so they must have had things in place to make sure an allomancer was not able to leave easily even if they did find a source of metal. They probably forced allomancers to burn that one metal every day that wiped out the rest of their metals in their stomachs, much like they did when they captured Vin.
Needless to say, given all the facts, I find it difficult to believe that there isn't a much bigger story that could be told. Kelsier somehow found enough metals to defeat 'many men', which was emphasized in text. He escaped from a prison that held allomancers, so they must have some precautions in place to make it difficult for one man burning trace metals to escape. Sometime after escaping, he took Gemmel as a master to train him to use his allomantic abilities, which despite the fact that he possibly killed many men using said abilities, still needed to be pushed off the wall. And Vin who had years of self training, appeared to be a quick learner by Kelsier's estimation, even though Kelsier himself would have had hours.
Who knows, maybe I just like Kelsier too much, but to me it seems that there is alot of info that could almost be a prequel in and of itself.