I installed the S1000 on our boat last summer. It worked really well right off the bat. This without me executing the "autolearn" feature, an actual plug and play install. The instructions were excellent and the install was pretty simple and straightforward.
However...the autopilot started doing funny things periodically, i.e not clicking in immediately or veering off to the right. I read about some of these idiosynchrosies on another site (THT) the other night. They call them "Crazy Ivans" for whatever reason. It wasn't a huge problem for me, I just need to spend a little more time adjusting some things and using some of the tips garnered from others' experiences. Apparently, this is correctable.
To be honest, the one thing I didn't like is, since I use it mainly to troll while salmon fishing, there are times when the GPS shows the SOG to be slower than 1.5mph, at which time the S1000 won't work. A lot of this depends on the how fast the current is and whether or not you're going with it or against it.
Regarding the pump noise, I installed it behind and below the helm. With the S1000, everything is installed close together near the helm. It is noisy but many times, if you're going fast, you don't really hear it with the engine noise and such.
For the price, it's a good unit but not perfect. It all depends on how you want to use it. I haven't really spent alot of time following tracks or using it exclusively to go from one far destination to another. I have used it in 2-3 footers and it handled it quite well. Would I buy it again? Yes, definitely due to the price point and ease of installation and use. It would be great to have a TR-1 for some serious fishing but I don't feel the need to spend $3000+ on an autopilot. The S1000 works out just fine and will work even better when I spend some time with it to learn how to use it.
Those are my thoughts on the S1000. Good luck on your decision.
Peter