Curious, are you rewiring and your new harness didn't come with grommets? Or are you just trying to change out the grommets on your existing wiring harness? That would be a challenge, but the grommets are available from TRF and Moss.
I have used Butyl Rubber ropes to mimic grommets in the firewall. It adheres to itself, can be smoothed over with spit, and stays permanently looking good. You can shape it to look as good or better than some grommets. NAPA sells it.