Jeff,
I also thought installing a cap would be straight forward, remove the console, glue on the cap, and re-install. Didn't work out that way for me either.
To get it to look and fit right I had to make some modifications to the original console. First remove the wood piece and boot. Once your done fitting the console cap it should fit right back where it was without causing a fit problem with the heater vents. I used a dremmel with a universal cutting bit (looks kind of like a drill bit) to shave off as much of the green foam and some of the plastic cover (of the console not the cap). It took removing allot of it to get the cap to lay perfectly over the console where you couldn't see the original console. You don't want any of the cap to stick up above the console or it will cause problems with the radio consoles fit. There's actually a metal frame inside of the console to use as a guide, so don't be afraid to go to town on the green stuff just remember to leave a good amount of the original plastic on the outside or you'll have nothing to glue the cap to.
I wouldn't cut the wood panel. Like you said it has a metal backing. The front lip of that backing sits on the front ledge of the console. Without it the wood will sag down onto the top of the trans housing.
Take your time and you can make that cap look good at a fraction of the price.
Hope this helps.
Rick