Does it leak when driving, or just sitting?
My CJ's either leaked from the cowl seal, window seal, around wipers, or the soft top to window frame.
Check to make sure the cowl seal didn't get folded over incorrectly when they replaced it or folded windshield down.
With fiberglass windshield frames, some have a poor fit and don't sit correctly on cowl. If that is the case you can build up the seal where it is leaking with foam pipe insulation. Don't use caulking if you ever plan to fold the window down.
Make sure cowl isn't rusted since they replaced the windshield frame, good chance rust was in the cowl. In picture yours looks pretty clean though.
Take a hose (we call it a hose pipe here in the south [emoji3]) and spray it all along cowl if you haven't tested it already. Just a process of elimination for water leaks.
Your CJ looks awesome! Makes me miss mine. Rust probably isn't a problem, but I would fold that window down and check everything.
That's my 2 cents worth of advice.
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