It has been raining a lot recently and I have begun to notice water pooling in my passenger side foot well. I have ran my name across the door it do not feel any wetness so I don't think it's a door seal issue, although I'm replacing the ones that are dry rotted anyways. Is it possible water can leak in from these holes in the engine bay firewall.

 

Check your windshield.

 

If it's getting through those holes, it should be easy to see some pooling in them when it's raining. I agree with the windshield recommendation. Small hairline cracks in the windshield or at the very edge/top of the windshield are usually easier to catch happening while you're actually driving, since more water will be getting pushed over it. I have a tiny leak in my XJ's driver side door because I need to re-apply some weather stripping. My truck has a tiny one from the top of the windshield. Both will drip a tiny pool of water if it rains a ton and it was sitting, but once I start driving it'll drip a bit, and I can see where it's coming from.

 

Apply some clear RTV to the holes if you thnk this is an issue.

Is your radio antenna external seal secure/alive? If not change it.

Climb under your Heep and look under the right fender wheel well liner. Is the floor board rotted out.

Look around mate. No one can inspect your Jeep over the internet.