Re: .and now my rear rim is screwed up....halp
If you have access to Sheldon Brown, you're on the right track. There are a number of other sites available also for reference with a search on bicycle wheel truing. Your idea of setting up an indicator is good. I've found it easier to use the front fork of another bike turned upside down for a truing stand. While I suppose it is possible to strip threads on spoke nipples I've never had it happen but stripping the hex on the spoke nuts is easy if you don't use the right size spoke wrench.
A question is was it that way when you got it or did something cause the wheel to be thrown out? There is a concern for caution because a wheel badly out of true can be subject to collapse. Good luck with it.