You could give the MessagePack protocol (http://msgpack.org/) a go. It's like a binary JSON with readers and writers in many languages. I've successfully used it on a server network running LuaJIT to transfer data around, and it's quite compact.
Particularly, q3map2 was developed by some very clever and knowledgeable people (John Carmack of id, and Randy Reddig of Splash Damage). If q3map2 is taking a long time to compile your maps you are very, very unlikely to improve on that with your own code. Four minutes is a long time for a map - which stage is it slow in? BSP, VIS, or lighting?
I use an ancient version of http://www.ultraedit.com (version 8.20a) which does everything you've listed. Unfortunately I can't recommend more modern versions because I have not had a good track record with them. There always seemed to be some show-stopper bug that made them unusable for me. However, I haven't found anything more comfortable for me than 8.20a. I did try both Notepad++ and Sublime for a month each but neither of them stuck.
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