Click, I can't say for certain, but I don't think your MM will get deleted if you cancel at the MM prompt during the full CD installation. You should be able to use both programs, although I personally never installed MM.
The DJ driver is what the DJ uses to communicate with the PC. The driver is not used to transfer files, but it must be installed for the DJ to work properly. To transfer files, you use DJ Explorer, MM, or MC10.
Given that you've been having problems getting the DJ to work with the MC10 plug-in, I think it is best to uninstall MM first. However, since you have MM working, I can understand why you may be reluctant to do so.
You can try with both programs installed and see what happens. But if you still have problems then you may want to uninstall MM.
Also, you mentioned some problems with your USB port. I'm not sure what is going on there. If you can transfer files using DJ Explorer, I would think you'll be successful with the DJ plug-in. If you have problems with DJ Explorer, then your USB port may be the problem.