The redemption ROM does not install itself on top of the version of android you have on your phone, it completely replaces it. Whatever version of android that redemption uses (im going to assume the LEAKED 4.0.4 from a few months ago) is going to be the version of Android you will be running, so really if you are going to flash now that you have received the OTA, waiting for the OTA was a moot point.
The good thing is the devs will be incorporating this new OTA into their ROMs shortly, so waiitng for an updated ROM shouldnt be too long.
Redemption ROM is based off of the AOSP version (build IMM76D). Lou builds Redemption ROM from AOSP, then adds the pieces to make the CDMA/LTE Galaxy Nexus work.
Anyways, OP, the Redemption ROM completely replaces your system. When you flash it, it will replace your current installed system with Redemption ROM, wiping your settings. Most of your content is fine, you will have to redownload your apps, but your settings are gone.
Redemption ROM is based off of Android 4.0.4, so in essence, no. It will not mess with your 4.0.4 update, as you will still be running Android 4.0.4.
Any other questions? Feel free to ask