The ST4000 control head is NLA from Raymarine and has been for several years. I'd hesitate to send it in to Raymarine and pay the $275 just for them to tell it's unfixable and replacement is not available. If the 'Navy Bean' is an off the shelf electronic part, you could order one from any electronics parts house. I'd take yours to a competent electronics repair guy and see if they can identify whether the part is generic or a custom chip before putting any money into the control head. I've found that usually if a part fails on one thing, it will also be failing or already failed on another similar thing. If the parts head is cheap, might be worth a try, however. If you can't fix the control head, you may be able to buy a brain box and control head for the X5 autopilot used off Ebay or similar site. Believe the compass and wheel drive for the 4000 autopilot are compatible with the later model X5. Know the RM 4000 plus compass and wheel drive work with the X5 brain box and control head.

As far as the water ingress, it was probably from the rear of the control head. The faces are supposedly water proof and the covers are for UV protection when not in use. RM cautions about exposing the rear of the instruments to water.