I did a clean install of lion over the weekend, I just basically backed up my home directory. I didn't need to keep any of my apps or settings and I wanted to repartition my hdd into two anyway.
If all you data is kept on another partition, I would erase the os partition during setup; this will likely remove all your apps depending on your setup but OS X version re-installs over the top on default. Create a temp admin account first, then recreate your account with the same short name as before. Then change your home directory of your account to the other partition, as no data files are created before the user logs in.
Once you login to your real account, all your data files and settings should be there; and your shouldn't have any issues with file permissions. If you do just run the file permission repair and that will take ownership. Then remove the temp admin account.
This is what I did when I moved from leopard to snow leopard on another machine that I no longer own... but it worked fine.
With your time machine, you can restore your apps my drag dragging them from the time slice apps folder to your apps folder as it is now, and as you have the programs plist file already in your library folder, the program should come back with the same settings.