Theres one method...
If you can run a VM, you can install a suitable o/s then winmx with that.
Windows 7-64bit offers XP mode, which is a good example, windows 7 itself will run one instance of winmx, and then using the XP mode, which is a VM, that will also run WinMX, thus the 2 instances of MX on one PC.
Other than that, I know of no way to run 2 instances, altho someone else may know of a means
Then you can run 3.54b4 for both instances, and have the best library options (why keep the old version anyway?)