Is there a way to modify the free play in toribash? I currently want to remove/lengthen the timer and/or remove uke.

You can't completely remove Uke, but you can type '/opt uke 0' to make him disappear (even though you can still touch him) and '/opt uke 1' to bring him back.

By timer, I'm going to assume you mean match/turn frames, because there is no timer in Free Play, hence the name. Just go into Setup - Game Rules and edit the matchframe and turnframe boxes near the top.

thanks