mod_fcgid: read data timeout in 31 seconds,

Uploading a new theme in wordpress produces this error..

Increasing Max_execution_time in php does not make a difference

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Howdy -- try going into Server Configuration -> Website Options, and there, increase the Maximum PHP script run time.

No Change...

I also changed the php.ini max_execution_time..

Does it at least change the timeout shown in the error message?

Yes

mod_fcgid: read data timeout in 121 seconds

Ah, it sounds like, for some reason, your application just isn't finishing within that amount of time.

You may want to try increasing it more, just to see if it finishes it the timeout is even larger.

Alternatively, you could try changing the PHP Execution Mode to CGI. It's possible that could help with the issue, or at least cause it to generate a better error message.