WOW that boat is CLEAN!
Congrats it was a pleasure to throw some advice out there. I'm currently on my boat, drinking coffee and watching tv at the dock. You're going to love it.
Some ideas on autopilot. I ended up installing a past generation Garmin TR1 which can be had for very cheap. I highly recommend it and have about $500 in my system which works flawlessly. It has all the features you'd want in a modern system too. It's basically Garmin's current production autopilot without the digital controller(has a push button remote). I searched far and wide trying to save money and can't say how happy I am to have this one.
My windlass is currently broken and I do miss it. It's next on my list.
If you do decide you'd like a Genset i've been looking because mine has been neglected but still working. You can easily buy a used 5kw for under $2,500. I'm in FL so cannot do without AC but if I could i'd love to see mine go for the extra space in the engine room to work.
Golf cart batteries are great and what i've chosen to install but make sure you check the fluid levels regularly.
That 165 will push the boat @ around 8 knots @ 1500rpms and mine tops out @ 11 knots. I run the boat @ 7-8 knots to keep noise down, it's extremely efficient @ 1500, and keeps the wake down. With a fresh bottom job and a lighter boat i'd be interested in your top speed. I'd guess 13 knots.
For purposes of haulout or just general knowledge the boat is advertised @ around 16,000lbs BUT i'm not sure how they got to this number because in my research of quite a few MK1's that have been weighed they come in between 20,000-23,000lbs.
Take care of the front hatch over the bedroom. Not only are they prone to leak but more importantly they are impossible to find and if you do they cost big money. Mine is shot and i'm honestly thinking about adding fiberglass to make the opening smaller/standard size. Similar story for the windows and sliding door.
While the boat is hauled out consider fairing the keel ahead of the prop. The info is in the thread posted below and the results are amazing for not much work.
http://www.trawlerforum.com/forums/s6/perkins-t6-354-best-practice-22543.html