Possible answer to Q1. A left-over registry reference perchance?
Maybe run a registry cleaner and see if that helps. But make a system restore point /before/ doing so. Then if it goes pear-shaped, you can step backwards as required.
I would personally run the Issues option in CCleaner first to see if it clear it. But if that doesn't do the trick, I'd try try something a bit more rigorous such as Registry Cleaner.
Q2. Sounds reasonable. But is it possible to rename the existing clone so that it doesn't get overwritten, just in case you need to re-instal the original? Safety first and all that. HTH.