It's TOTALLY worth it to do the head unit, IMO. Just that made the system sound tons better. Because the display center very easily pops straight up, you end up with a nice amount of room to work with. The woodgrain trim surround has two screws which are directly beneath the climate control module. Be gentle and use a trim removal tool if you can, but the climate module pops out really easily without having to remove the knobs/buttons if you have heated seats. Remove the screws and then (if you have one) use the pry tool to release the clips on the trim ring. I tend to work a little at a time, first around the shift knob being aware that there's a ground wire that will need releasing near the shift knob on the trim surround. It has some slack, so just be ready. The clips are located kinda mid shifter area one per side and then towards the center of the stereo hole one per side. Just take your time and be gentle because the edges of the trim piece are fragile. Try to get the tool more into the center of the trim surround to avoid chipping the edges.
Once you go in there a time or two, you'll find it absolutely no big deal. There's plenty of metal supports in the dash to get a nice, snug fit with big zip ties. It just takes patience... but it is monumentally worth it.
I ended up doing this twice because I did just the head unit and speakers and then decided on new amps, woofer enclosure and new wiring. I did not bother with satellite radio or a backup camera because I'm into MP3s and don't care. Backup camera on an Aviator/Navigator, sure. On an MK8, not for me.
If you think that you may ever wish to upgrade the amp, you may consider running your RCAs and remote turn-on to the amp tray in the trunk. Not difficult and you'll have everything there for the future. There's a great cable tray just beneath the carpet that I ran all my stuff through next to the passenger seat except the 4 AWG for power from the battery. There's plenty of room in there for speaker wires and RCAs. This way, unlike me, you won't have to uninstall/reinstall the head unit for this upgrade like I did.
The head unit install time with the JBL adapter is really probably a couple hours max, most of which I spent on the best way to route the zip ties. I took my time with my entire system install so as to solder everything, take great care with my aging trim pieces, run the power thru the passenger side firewall to the amps, etc.
Lastly, if you just do the headunit and don't plan for future upgrades, it is MONUMENTALLY easier to remove the trim surround and access the head unit for redoing because now you're a pro. Also, my second attempt at securing it was much better. My airbag unit fit so snugly to the left of my head unit that I don't think it needed securing. It's covered with a neoprene type material and is very light.
To me, any upgrade to the aging stereo system is totally worth it. The speakers are super easy to upgrade, even if you don't do the wiring just yet and are totally worth it.
Good luck! If I left anything out, I'll try to check back here. Also, Trippen is serious when it comes to stereo installs and very likely has excellent troubleshooting advice for you. This is just how I did mine.