Myguggi's suggestion is the same as your 'Method 2', so you should expect the same result.
Roxio has built a sort of 'reverse gear' into their installer which you might describe as running the installer backwards. It might do the job for you since the Windows uninstaller has failed.
Method 4: You copy the Program files off your installer DVD or software download into a folder on your hard drive, and put a copy of CleanSystem.bat into that same folder where you see Setup.exe.
Then you run CleanSystem.bat by double-clicking on the file, and it runs the Roxio setup in reverse. Here is a copy of the batch file. CleanSystem.bat
I'm hopeful that this will work, but not really confident since the MS uninstaller has failed. Still, it's worth a try, I think. If it fails, you might need to go to method 5.
-Download the free trial version of the Revo Uninstaller, from http://www.revouninstaller.com/
-uninstall all Roxio software. When you highlight the software to uninstall, right click on it and choose moderate mode
Once you have cleaned NXT 4 out of your system, I don't think there will be much point in trying to put it back in. If you get the Feature Update 1709 installed (and if you refuse it Microsoft will hold you down and force-feed it to you because the medicine is now compulsory!) from what you've said 1709 doesn't like VirtualDrive. Roxio's custom installer doesn't allow you to de-select VirtualDrive because it's integral to the suite, so you're stuck! As you see in the screenshots, VirtualDrive is the droid you're looking for, not Roxio Secure Burn. Sorry, but I can't see a way around this.