Good stuff Paul. Fun journey fraught with danger. Being methodical will get the results you are expecting...and you should be expecting the worst. Build in as many fail safes as possible from the obvious roof closure through to watchdog timers on pc's so that when they freeze or crash the bios automatically reboots them.
Sounds like you've got all the right gear to make it happen, and the important glue to make it all work together harmoniously with CCDautopilot. Great software, shame there's still no web interface. If you are looking to move beyond automated and get into robotic where you upload plans and out spits data (everything in between is handled such as when to shoot the target, close and reopen the roof as bad weather has passed), ACP with Scheduler is your answer. Not cheap, but its depends on what you want to get out of your set up. Includes PinPoint so no need to purchase it separately.
Talking PinPoint and platesolving, playing with ACP 7.0 the other evening refining polar alignment. The ACP script SyncLostScope is an absolute cracker. Within TheSky ASCOM settings, turn off inhibit sync to protect tpoint model, run SyncLostScope script which platesolves using Astrometry.net i.e. it will platesolve literally any part of the sky even if polar alignment and pointing are way off. Once Astrometry.net returns a result, ACP cross reference this with a local catalogue i.e. GSC or USNO-A2.0 then sync's the scope. Enable inhibit sync to protect model again and you're off ready to do another tpoint run with AAG Tpoint mapper. No more trying to find a bright star to first sync on which can be an absolutely pain in the backside at long focal lengths with no finder scope. 4hrs later, 305 points mapped.
I'm looking forward to seeing the productivity levels rise as your adventure continues.
