Jim:
Actually v41 does have an "uninstall". Unless something really trashed your files you should be able to go to START->SETTINGS->CONTROL PANEL->ADD/REMOVE PROGRAMS scroll the window down to find "v41" and click on the "CHANGE/REMOVE" button.
I've run v41 on all Windows O.S's from Win98 to XP professional. It is true that Win2000 needs one different file but Warren does provide instructions. Windows ME--for me--installed both the current vs.7 and the vs. 8 beta without problem with the current installers available on "the other site".
Also, if you just uninstalled the font file and the executable you probably haven't cleared all the used files.
Even clearing the program's folder--usually in "Program Files" may not clear all the ".dll" files as some could be left in the Windows or Windows/system(32) folders.
The best way to clear out everything is to download the latest files then install them. Because font files and dll's are considered system files be sure that in a ME system the "System Backup and Restore" is turned off before you start. This is Microsoft's way of protecting us from ourselves and will save and restore system files it things you shouldn't be deleting. If you delete a "system" file--outside of an "unstall script" -- the OS will often save it and restore it. It can even "restore" over a newer, just installed version.
When the installer asks where to install to: be sure that the new install is directed to the existing program directory. After this do a re-boot (it's Windows after all!) and then go to the control panel and uninstall the program. Re-boot again, and check that all references to v41 are removed from the system: any lingering folders, etc. Oh, also be sure you purged the "Trash Bin" so files are really gone.
Finally, reboot again (you know, Windows!) and then run the Window's "Error Check"(i.e.scandisk) tool and the defragmenter tool.
After all this you should be able to re-install the latest version without problem.
By the way, don't blame Warren's software. Things like this are generally Window's problems and as with most Windows problems are a b.tch to fix.