Welcome to the club.
Couple minor things to note:
For your head unit, do you have the Rockford Fosgate system in yours? If replacing the stock head unit, most of the audio sites recommend the wrong Metra harness (unless they finally updated it). The one you are looking for needs to have the RCA plugs, otherwise your amp will be super loud and have tons of distortion, as you need to connect it to the pre-outs on the head unit rather than speaker outs.
I'll keep that in mind, but it's already got an aftermarket head unit. Judging by the quality of the other mods it came with* I suspect the original harness has been cut and I'll have to wire it all from scratch. I haven't checked what harnesses are needed for speaker upgrades, but are the online suggestions correct for those? I'm going with coax so I won't need to worry about replacing the tweeters.
For the keys, you might want to take this opportunity to go with the Rogue mod. Older Rogue keys have the keyless remote in the head of the key itself, and it is compatible with the Xterra. Super handy as you now don't have a separate key+fob hanging off your keychain. As long as you can get the key cut and transponder programmed, the wireless entry part can be done by yourself.
I saw that in the HOW-TO's (been creeping the forums for months now) but I think I like the separate dongle a bit better. I keep my car keys separate from the rest of my keychain anyways.
Tonight I reinstalled the battery, restarted it for the first time after oil change and plugs, rechecked the fluids, and pulled the driver's seat out to clean the carpet and RF subwoofer under it. Installed some MaxSpider mats while I had the sub out because they're too big otherwise and needed to be installed underneath it.
*Found some remnants of a chinese HID kit under the hood, bully dog coming out of a hole in the dash supported only by the HDMI cable, stereo mic not secured to anything, disintegrating block heat plug, etc.