Hi Tug,
What you're running into here is a the technical issue of working with a corporation and not a technical issue with the physical parts.
When BayStar first came out we started using them on C-Dory 22s both with single and twin engines and with and without autopilots. Receiving the very first BayStar kit resulted in an immediate call to SeaStar steering (Teleflex) to find out why they said we couldn't use the BayStar system on with twins or with an autopilot. Thankfully I had gotten to know the techs in BC pretty well over the years so I felt I could count on a straight answer and I got one.
The situation is that when the BayStar system was developed it was to fill the need for a hydraulic steering system for smaller boats and at a much lower price than their SeaStar system; boats that traditionally (and typically) do not have twins and/or autopilots so Teleflex had no motivation to develop kits for that use. Because they don't supply kits to add a second station or autopilot, and because they don't make a tie-bar for twin engine installations for BayStar steering cylinders, their corporate position is that the BayStar isn't intended for that use. In other words, if you choose to install an autopilot and/or twins they can't tell you how to do it or support it because they don't make kits to support that use (or write instructions for on how to do it).
It is not a physical limitation of the hardware itself, just the lack of support (purposely) by Teleflex. They told me right up front that if I could develop the means to add in an autopilot or how to arrange a tie bar for twins that they had no issues with the steering system being used in that way. In fact, the BayStar helm does come equipped with the third port that the balancing line to the autopilot pump needs (just as it is on the SeaStar system).
If you decide to mount the S1000 steering pump as suggested in the S1000 kit you'll have everything you need for a successful install. If you decide to mount the S1000 steering pump at the transom it will take a Teleflex HF5501 Add-A-Station kit and a bit of wire (to lengthen the wires from the S1000 brain box to the steering pump).
We've been installing BayStar with twins and autopilots for around 10 years now without issues. The early BayStar helms (molded material) did require resealing more often than should have been the case; the new helms are aluminum and hold up much better. We also have to replace seals in the SeaStar helms so they're not immune by any means.
Hope this will help you with your project.
Regards,
Les