Great questions, and a great way to learn more is by looking at and actually planning out how to buy actual assets, even if you end up passing on them.
For your questions:
* I do have a down payment for a property this size, but I'm fuzzy on the exact percentage the bank is going to expect. Is it 20 or 25% down?
It depends on the lender and the property, you'll see in the 65-85% LTV range, with 70-75% being most common. Just start collecting lender quotes, or get one broker who can shop a lot of lenders.
* How many months worth of expenses do I need to tack onto that to make my numbers work?
Plan on 12 months of principal and interest in cash reserves. A Fannie/Freddie loan will actually take this cash and put it in escrow. You won't be able to get a loan like that as a first-timer, you'll need a partner who has done that loan before and then sign on it with them. For bridge/private/bank loans, they'll want to see net worth of at least the amount of the loan and liquidity as 10% of that loan amount. For conservative underwriting, working capital of at least $1,000 per unit unless the complex is really large, is a good starting point. You'll need to pay for your own construction on a Fannie/Freddie loan, or with a construction/bridge/hard money loan you'll pay up front then get reimbursed for the construction costs
* Is there anything like a pre-qualification phase like there is with a residential mortgage?
You can get a letter from a lender to show to the seller/broker to help your offer. But there's no seasoning of funds on commercial loans. They're private and less regulated, so you'll see more variety in terms, however.
* For the more experienced among you, what is an instant deal breaker even if everything looks good on paper?
If the numbers are good, I'll go through a lot to make a deal work! Deal breaker is if I'm not able to raise capital or find someone who can sign on a loan if I don't have the net worth or cash myself. Another one is if the building inspection throws my numbers with unexpected repairs and seller refuses to retrade after not disclosing those issues up front. I also don't like rigid sellers who will not work with me to get reasonable extensions for lending and capital raising: I want them to be in it with me rather than itching to move onto the next buyer. If the purchase and sale agreement PSA is really seller-sided, that gives me pause. No warranties, low liability limits, rigid timelines, no extensions pre-negotiated, hard EMD up front for an older building I haven't vetted yet that they won't disclose on, stuff like that.
* If I identify a possible deal, is it bad form to reach out to the property manager directly and ask about the property's pain points?
The broker will get all this info for you, or if direct to seller, you just ask first. If the PM doesn't know it's for sale, you could be in hot water with the seller.
* Are there any regulatory burdens I need to be aware of for properties of this size?
All I can think of is fair housing and state tenant laws like evictions, support animals, etc. Know the laws! In Landlord friendly states, it's pretty easy
* What tips do you have for building a team and systematizing stuff.
Systems is just a word that makes a to-do list sound fancier than it really is. Create to-do lists, and you'll start to see patterns. Make those into standard operating procedure SOP lists. You'll be building spreadsheets and lists as you go along. Don't over-systematize before you know what you're doing, you'll likely change it anyway as you learn, and don't get too rigid where you can't be creative in solving problems. If you're disorganized, get some help with an executive assistant VA or intern; if you're a compulsive checklister, remember that things are always changing, so build in some flexibility.
* Where do I go other than LoopNet to shop for apartment buildings?
Crexi, contact all the brokers you find on those sites. Direct to seller for buildings this size by doing skip trace searches to track down LLC owners and contacting them or their attorneys, calling on hand made for rent signs is usually an owner. Larger properties the best source is brokers. For me, what's worked best is hanging out in places where owners hang out like REIA, conferences, so when they're selling I get first look.