EDIT: I discovered the creaking is actually comming from around the upper door frame (which seems to be very flimsy), I have tried adjusting them by hand, and it doesn't seem to do much, I don't kow weather to pull the frame away or push it in? My seals look alright, I had just lubed them with silicone spray. What is the fix for this?

That creak could be any of numerous things interior to the dash board. That'll be a real witch hunt trying to track that down. Not much help here except for removing the dash all together for close inspection.

I think the weird thing is that its only when I take off or I stop, it won't do it over bumps

Mine did that too after I got my windshield replaced.

my bose amp creaked when it wasnt tight

EDIT

Any Suggestions?

I got a squeak/creak when I changed the endlinks. It went away when I changed the struts and mounts.. it'* tough to say what will fix a noise like this.

Just have to try different things unitl you find what works, or something else becomes louder.

Did it do it before you put silicone spray on the weather stripping? Sometimes, a light coating can cause rather that solve squeaking. Try a heavier coat of the spray, or some silicone grease and see if that helps.

well i took a mallet and lightly pounded the upper door frames in, and it seemed to help quite a bit, although there is still some slight creaking when braking comming from the doors and dash