I feel like it's weird that toms aren't essential to whatever your end goal is, but jazz brushes are. Ultimately, your choice though.
SM57 is fine for snare, but for overhead, use condenser mics. They're a lot better for that sort of thing.
Never played on a Millennium pedal before in my life but if it's only 522 SEK ($55 roughly in USD) that shit is monkaS. Definitely pay a premium for a good pedal, it'll make a massive difference that will certainly be worth it.
I'd recommend get a drum key plus some heads. I use Evans Genera Dry and Evans EMAD2 with corresponding reso heads. Remo and Aquarian make their own versions, but they're all good from my experience. They make a world of difference, and if you go the used route, will probably be required depending on the condition of them.
This is definitely subjective, but in my opinion, there are shitty cymbals and good cymbals with no real in-between (with few exceptions). 101 to PST5 is an upgrade, but both are pretty shitty overall. As long as they aren't cracks (maybe keyholing depending on how bad it is), 100% look at ebay for that because shipping won't be ridiculous compared to full drum kits. In general, you can skate with a crappier hi-hat and ride, but I would pay a bit extra for a good crash.