The existing alternator bracket actually worked with the larger Wrangler. Wrangler NW also sells new brackets. The regulator is installed up high on the inside fender. Load test batteries to determine condition. Lousy batteries wreak havoc on a charging system.
Poor batteries shorten an alternators life.
Replace frayed wires and undersized battery cables. Remove alt clamp on battery cable repair ends. Replace with Heavy Duty, high quality parts all available from Wrangler. Check out Wrangler's custom crafted fine strand copper cables. Upgraded cables will give the electrical system a giant boost in performance and reliability.