I've seen soft top patches in the auto parts store before. I would try that.
2013 JKR, Commando Green, 6-speed, soft top
Mods Complete: ACE rock rails, AFE high tuck axle back
Mods To Come: 2.5" lift, aluminum front & rear bumpers, winch, Trailready wheels, 33's, Quad Stealth LED headlights, Inspired Engineering or Quad LED fog lights...