You have very similar needs to a position I held recently, for a whopping 3 days duration. I lost that job in part because I didn't meet the owner's needs. But also because they didn't want to hear what I had to say. So let me tell it to you, now, before you end up buying a shiny new instrument, and expect all your problems solve themselves.
You will have to analyze a pharmaceutical to a standard required by the government. Briefly, you will not be permitted to buy a fancy machine, say that it worked once, and analyze samples the same way, and say you're producing a product that is to the proper standard. You will have to validate your system according to system suitability. That means you will have to run standards, traceable to a government standard, at least every day, if not every time. Control samples, prepared in the same way, will have to flank your unknown samples to be certain the system remains in calibration from sample to sample. That's (part of) what system suitability means. Validation is performed (in part) by deliberately deviating operating parameters by 10 % and proving that the results aren't affected. You may also be called on to perform real-time and accelerated stability studies, to prove the pharmaceutical survives ordinary or harsh storage. This is basically a PhD level job, for someone with very specific experience. Their ability to run a GC-MS is actually trivial, compared to being experienced in the tasks I've outlined above.
Microbiology is totally different. This is likewise, a very advanced skill-set, totally different, yet still held to the same standard. Microbiologists work very long hours: preparing media, and dilution solutions, and preparing to take a sample. When they're ready, and only when they're ready, they begin to take samples, and incubate them to see if some microbes grow, how much grow, and what microbes are growing. Only then can they give an answer as to whether the samples meet government standards. Often, they work in another room, where people who don't have to work aren't permitted to enter -- microbial contamination caused by the boss coming to chat them up will ruin all their work. There are automated machines meant to perform such analysis, but they still need people to follow basic rule, in addition to being knowledgeable in their operation.
I'm a little bit worried for you, because you seem more than a little unprepared. Let me give you a tip -- the $15,000 USD Ebay GC is almost certainly so broken down that it will not work. But the brand new $150,000 USD one will not solve all your problems just because its expensive. You say you're outfitting a laboratory -- do you have a functional laboratory already? Do you have volumetric glassware, an analytical balance, a distilled water system and an autoclave? You will need these things to support the functions you want to perform.