Okay, so I'm away from that computer, but I have found a partial workaround.
The biggest problem for me is the windows/alt keys being reversed. Those can be switched in the keyboard preference pane. So, of course, it will ALSO switch the keys on any mac keyboard you have connected, but for me the command key being in the right place on the ergo keyboard solves 80% of the issue right off.

Now, beyond that, I'm not at my work computer so I can't attest to the other solutions I found. Both are keymap helpers. Besides the command and option keys being fixed, the number keypad is the next biggest thing that needs to operate for me. There is a preference pane called doublecommand. It's at http://doublecommand.sourceforge.net/index.html I installed it on my macbook here and it appears to install and work on EL Capitan... though I have no access to the MS keyboard here, so I can't verify completely it's functionality.
The other key-remapper is now an app called Karabiner. https://pqrs.org/osx/karabiner/
Haven't installed it, but my try tomorrow AM in order to get other functions working if I can't get joy from the internal OS X preference pane and Doublecommand. If anyone has success or failure to report, I'd love to hear about it.
Regards,
Bill