Thanks everyone for your advice, here's what I found out after re-reading the contract for each of the points you raised:
Continuing ed costs - the time is paid at base salary, so while not technically paid for by the clinic, she still gets a paycheck including the week of conference.
401k - they have one, but there isn't that much detail in the contract itself. I'm going to see if we can have the clinic contribute employer max to it. We won't miss that money, and will invest the equivalent of the tax savings into my 401k. Eventually, will roll the 401k into a Vanguard IRA when we move after my training finishes. Does that seem like a safe plan?
Vacation/sick days - they are 2 weeks per year and don't accumulate every year. However, they will pay for the hotel for vacations! I'm going to see if they'll just give us some money if we stay at a budget hotel like sane people.
Contract termination - This says 90 days, which sounds like the standard for physicians. Good point about severance, there isn't anything about that other than they will pay the remaining 90 days' salary. What is COBRA, I didn't find it in the contract.
Non compete covenant - she wouldn't be able to work within 10 miles of the clinic for 3 years, which isn't a big deal for us. My hospital is just outside of the radius, so she could potentially get a position there if needed (but pay would be less).
Equity - no equity, she gets a salary plus the other benefits only.
Overall it seems like a good deal. I'll have to ask about cobra and the vacation payment. Thanks everyone.
