In my experience with these old heaps, there are four areas that allow water into the passenger area.
#1 is the easiest to fix. The cowl drain can become plugged with leaves, dirt and other debris. Simply remove the fat hose on the firewall by the battery and clean it out.
In your case, I doubt that that's the cause, but cleaning the cowl drain takes so little time that it's a good thing to do "just in case".
#2 is what I find to be the most common cause of water leaks. That's rust on the windshield frame behind the rubber molding between the glass and the frame. Water stays behind the molding and causes unseen rot holes, then water seeps in through the holes, down through the wiper gallery and onto the floor. The cure for this is replace the windshield frame.
#3 is as you suspect on your Jeep, a leak at the cowl gasket. The cure for this is to replace the cowl gasket. The aftermarket gaskets are reputed to not fit properly. Make sure to buy an OE gasket.
#4 is the seam on the cowl between the horizontal and vertical pieces that make up the cowl assembly. If you see that the factory caulking has deteriorated and cracked, it's an easy fix. Simply mask off a 1/8" area along the seam and seal it with clear waterproof silicone caulk.
As far as removing the torx head screws, apparently the factory used threadlocker (Loctite) on all torx head screws and bolts. You need to heat the bolts to break the bond of the threadlocker. A #2 tip on an oxyacetylene torch works quickest. It's almost certain to burn the paint if that matters. A plumbers propane torch should make enough heat to loosen the bond in a reasonable amount of time. The plumbers torch may or may not blister the paint, depending on how patient you are in building enough heat to do the job.
A butane torch might do the job, but just take longer than the propane torch.
A heat gun might do it if left pointed at the hinge from close enough and long enough.
For the tools, you'll need a properly sized torx bit. Once you think you have the correct bit, try the next size larger bit. It's real easy to make a mistake and use the smaller bit and strip out the teeth of the bolt head.
You'll also need an impact driver. A hand held impact driver that you whack with a hammer works best. Harbor freight has them for around $10.00. I use a pneumatic impact wrench but it's easy to strip the bolt heads with the impact wrench. The hand held driver works best because it drives the bit deeply into the bolt head and the shock of whacking it with a hammer helps to loosen the bolt from the grip of the threadlocker and corrosion.
Quadratec has the torx bolts. It's way more economical to buy a pack of 25 or so than to buy them individually. Jeep used the same bolts on the door hinges and on the roll bar struts to the windshield frame.
As you see on your hinge, the cheap torx bits shatter. I don't buy many Snap-On tools, but I do buy Snap-On torx bits.
Once you have the bolts broke loose, you can use a ratchet and socket with the torx bit in the socket to completely remove the bolt and when you're done, to install it firmly but not tight. Use the impact driver for the final tightening.
With all that said above, you don't have to disconnect the hinges to replace the cowl seal. Just unbolt the spreader bars (struts) from the roll bar to the windshield frame and the two large torx bolts that connects the "mickey mouse" brackets to the dash. The windshield frame should fold forward, giving access to the gasket. I suggest soaking the hinge area of the windshield hinges with penetrating oil for a few days before attempting to fold the windshield frame forward. The hinge pins rust and make it difficult to fold the windshield frame forward. With the bolts out. if the windshield frame is difficult to move, work it back and forth and keep spraying the penetrating oil as you work it.
Let us know how it goes.
Good Luck, L.M.