You have to open the programs menu (press the FreeCiv -text at the top bar) and there you will find the normal options.
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I have found a few bugs:
1. You can't change any setting graphically because the textboxes and checkboxes aren't visible in the settings. And no, there isn't a scrollbar, I checked. The only way to change settings currently is by writing "/set <values name> <value>".
2. There isn't actually any meu in the game once you start playing. Currently you can only do things like build roads or cities with keyboard shortcuts (wich at least I can't remember).

Anyways you have done great job so far on this and it's already more usable than the old port.