If there is one thing the Steam version got right was to include a modern control scheme preset. I'm getting alot of weird glithchiness with the menus and the mouse pointer not syncing right so navigating the menu was a bit of a pain. This helped sort things out quickly. Hopefully it will for you too.

Just drop it in your CONTROL folder and in game, select LOAD CONFIGURATION.

Dark Forces II
https://mega.co.nz/#!BoNAnBqR!4cdiRu2N5QAooQuAB0CdFGrETqOu7IkGdFgIWy3-prA

Mysteries of the Sith
https://mega.co.nz/#!dsV1nRRY!_dPEx72CE7ngjZficC0BLqXux3IrJM0jKFO6dBwjICI

In case it hasn't been posted already here's a patch that lets you switch weapons with the mouse wheel.

[url=http://www.jkhub.net/library/index.php?title=Addons:JK_Mousewheel_Support]http://www.jkhub.net/library/index.php?title=Addons:JK_Mousewheel_Support[/url]

does any of this include inverting the y-axis? It kinda grinds my gears that there's no setting for that implemented in the game...

There is....

There is! It's under the mouse settings. This preset will also sort it out though.

The links in the OP are offline. Could someone re-upload the files? Thanks!

https://www.dropbox.com/s/0hu8uuyh5zbrpwu/JK-Mots%20modern%20control.zip?dl=0

Thank you!

Thanks! This fixed the last remaining control issue that I've found.