Wow--that's some rough audio. I'm no expert on the R-09 internal mic, but I suspect that the show was just too loud/you were too close for the mics. Was it a pretty loud show? Was your rec level set to 1 or 2?
My advice--get some external mics that can handle more spl's, and don't have to stay in your pocket. Will you be going stealth mode, usually, or can you get something bigger and go with a stand? What's your budget? You can probably find a pair of Nakamichi cm-300s for pretty cheap, and because they are powered by an internal battery, you can run them straight in to the r-09.
As far as removing the pops, several audio programs have pop removal tools that might help, but I wouldn't bother. I'd just get out there and try again with a different setup.