Cutting away the rubber roof material is a bad idea in my opinion. The leak is most likely where the satellite antenna is bolted to the roof. Remove the antenna mounting plate and reseal the area with DiCor or Eternabond tape; then reinstall the antenna array.
For large width eternabond try:
They make sheets up to 4 feet wide if you have already cut a hole that big.
Lou and Laura with Bella - German Short Hair Pointer
2008 GMC Sierra 2500HD Crewcab SB Allison Duramax
2010 Flagstaff 8526RLWS - Superglide 3300
HAM CALLSIGN - KC3FFW