So my truck has been leaking for a few months now and I can't quite figure out how water is getting in the cab. I know it's running down the inside of both A pillars to the corners of the firewall and down into the track where the speaker wires run to the rear speakers.
There are some small holes and cracks in the paint in and underneath the rain gutter.

I have a brand new windshield and the rain gutters were sealed with silicon.

Does anybody have any idea where the water might be coming in from? And is there something better to use than silicon around the gutters?

 

I would suspect the windshield seal. It's not that uncommon for new w/shields not to be sealed properly.
Unless there were rust holes under the w/shield trim that didn't get repaired ?
If it started leaking after the w/s install, take it back - that's warranty.
If the body is sealed up good with silicone it shouldn't leak. Recheck your seal job and then check for leaks with a garden hose. Test the lower stuff first, if no leaks there work your way up a little at a time till you find the entry point.

 

It leaked before the windshield job. that slowed the leak on the passenger side but didn't stop it or affect the driver side. The body wasn't rusted under the windshield, only the clips that hold the trim to the truck and they were replaced.

When I get time next week i'm going to pull all the sealant out of the rain gutters and try some bed liner in em

 

I had a similar issue on my old 93. It was coming in from somewhere in the cowl. however i ended up replacing the door seals from LMC truck. I put a fog machine in the truck and closed it up, let it run and you'll find every single place water may be coming in.