I must say your obsession with tidiness is contagious.
I must do this one of these days when I find the time. Great to hear that everything is running smoothly despite the changes you've made.
Hoping not to complicate matters (that's why I didn't mention it in my previous post), you can actually keep your Scenery directory outside of FS all together.
Example:
On your C: Drive you create a folder named 0Scenery. The 0 is a Zero. Instead of having your scenery add-ons in the Program Files/Microsoft Games etc., you have them in 0Scenery.
Of course to do that now would be self-punishment

- I thought I mention it if you ever do a fresh complete new install of the sim.
I read about this once and tried it and it works perfectly. The old hands with slow, old rigs but plenty of logic came up with this.
Apparently the biggest hurdle concerning FS2004 can be the FPS... caused by the fact that as you are flying along, scenery has to be refreshed. To achieve this, the CPU (and or GPU?) have to work hard to get all the way to the place on the platter (your HDD) where the scenery folder by default and Microsoft's eternal wisdom is tucked away. Let's just say it's not a handy place to get to.
Now, having created a Scenery directory preceded by an 0 (Zero) this 'Scenery' folder is now on top of the list and the old rig can access the scenery easily.
I've been running both, FS2004 and FSX ever since FSX appeared. when I got a new computer some months ago I went a step further. Again the inspiration came from friends in the community.
Since MS Vista we have the additional problem of the UAC which has been partially carried over to W7. Apparently this can be a real problem with FSX. I cannot verify this as I changed my settings from the start. The problem they say is due to the UAC some (payware) add-ons have trouble communicating with the sim
particularly if the sim is installed in the Program Files directory.
Sooo... to avoid all kinds of hassles, I installed both sims, FS2004 and FSX not in the Program Files directory, but in two directories I created instead.
Thus, if I open my Explorer now, I have two entries on top of the list -
0FS2004 and
0FSX respectively. Works like a charm, never had any problems, even most payware self-installers find the sim(s) - if they don't, we know what to do.
Happy simming