SymLink Advice - Macro's/Settings.

I've read a few posts about SymLink and will be going this route shortly.
I'm pretty sure I can do the SymLink stuff, so its more advice on organization of my files and preserving settings then how to SymLink.
Any advice or suggestions is appreciated.

My main concern is retaining my wow/addon settings and macro's for my accounts.
My current set up is:

C Drive (Raptor 10,000): Wow A, Wow B, Wow C
D Drive (Seagate 7,200): Wow D, Wow E.

Wow A is my original install, with the directory renamed.
Wow B-E was a copy/paste from Wow A.
With 3.x ... I deleted the Addons, WTF and saved variables (except auctioneer) for each directory and configured each individually.

I'm planning to use Wow A as the full install, because the registry likely points to this as where the game is installed.

Would I be best off deleting the folders which will be SymLinked in B-E and then linking from A; or
Should I have World of Warcraft (full install) and SymLink to A-E directories (ie rename A back to original name, and then make a new Wow A folder for SymLinking)?

I made a copy of my wow A and then renamed the original World of Warcraft.
The new copy has been renamed wow A.
Then I moved wow D and wow E back to my C-Drive (faster drive) so all copies are here now.

To be safe, I cut & paste the Cache, Data, Interface and Screenshot folders out of the A-E copies.
That way if necessary they could be restored.

I then SymLinked Cache, Data, Interface and Screenshots from World of Warcraft to A-E.

Keyclone can start the game fine and Shat runs a lot smoother then it was before.
My only issue seems to be modifier keys. Prior to SymLink I could Shift Tilde quickly, for Ghost Wolf on all shaman's; with SymLink if I use a modifier key quickly, half the clients do not pick up the modifier key only the Tilde.
I can easily work around this, by putting combat functions on non-modified keys and less used functions on those that use Alt, Control or Shift.

I'm curious if this is typical for SymLinking.
Shat is much better then it was before, way higher frames per second across my clients.
So I do see very good improvement overall, but have the modifier key or perhaps combination of keys issue.

Any thoughts?