1) Right click drive or folder
2) Properties
3) Security
4) Advanced
5) Ownership
6) Edit
7) Select your user or group... even if Administrators owns the base folder, other sub files/folders could be owned by the user on the other computer, meaning you can't change permissions on those yet
8) Click OK and wait. It will take awhile and use 100% CPU. Hooray.
9) Close out Properties and open it back up... Security again
10) Edit
11) Add
12) Your username, or group, or "Everyone" to include Guest users. Note that the last choice will also apply to network shares accessing the folder so be careful.
13) Check Allow Full Control
14) OK and wait.
Done! Repeat as needed.
If you skip steps 1-8 you risk running into "Access Denied" prompts which will pop up once for every. single. occurrence. When you run into TortoiseSVN-created SVN metadata for a checkout it will happen A LOT. Your only other option is to cancel the entire thing and start over at step #1.
There are two ways to keep from having duplicate copies of apps.
1) Have a third partition with the same drive letter under both OSs, and install all programs there. Then you don't have to worry about paths in files on disk being different. (This is what I do, but I planned ahead.)
2) Use mklink /j in Command Prompt to make a junction from the same location on one drive to the other. mklink /j C:\something D:\something will make a folder called C:\something that will always mirrors the contents of D:\something without taking up any space.
Can't keep registry settings mirrored, but for AppData, Use mklink /j again to keep folders synced across OSs.
Here's the folders of interest (don't mirror these, just mirror individual app settings folders) and their counterparts in each OS:
Windows 7/Vista: C:\Users\<User>
Windows 2K/XP: C:\Documents and Settings\<User>
Windows 7/Vista: C:\Users\<User>\AppData\Remote
Windows 2K/XP: C:\Documents and Settings\<User>\Application Data
Windows 7/Vista: C:\Users\<User>\AppData\Local
Windows 2K/XP: C:\Documents and Settings\<User>\Local Settings\Application Data
Windows 7/Vista: C:\Users\<User>\AppData\LocalLow
Windows 2K/XP: C:\Documents and Settings\<User>\Local Settings\Application Data (? Not sure... there is no equivalent... so the app will probably pick a different location based on OS. I have to test this because the QUAKE LIVE BETA WHICH I JUST GOT INVITED TO AND HAVE 4 INVITES TO PASS OUT TO OTHERS uses it)