When in campaign, I unlocked Mechjeb, initial options like Delta-V, Orbit information and Surface information were available. After the next level of unlocking more Mechjeb options, these options are no longer available. The only options are the custom window, and settings. I've unlocked all but the 5 rightmost levels of the tree and still none of these options appear. I uninstalled and reinstalled Mechjeb, didn't fix it.

Sounds like your config might have gotten messed up somehow, the default
windows are after all nothing but custom windows. You could just
re-create them in your own taste or just try re-adding them, there were
presets in the window editor at the bottom if I'm not mistaken.

Closing this as an old MechJeb issue. Many MechJeb issues have had little interest in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is. This issue is being closed for one of those reasons. We apologize for any inconvenience, but keeping the TODO list tidy helps the developers.

If this bug/issue is still a problem, please open a new issue. For bugs please try to include a Minimal, Complete, Verifiable Example that explains all the steps required to replicate the issue. A link to the KSP.log file should be ideally included, but is often not sufficient information. Screenshots or short videos are often the best way to show a bug.