Bandito,
When I designed my HERMS I originally intended it to be a set & forget arrangement. The first couple times testing it, however, made me realise that set & forget just wasn't feasible. There are a lot of things that can go wrong - your mash can set (no runoff), the pump can fail to prime, a leak can develop or the valves can get get stuck in the wrong state, etc etc etc. Not to mention the times when you want to extend/shorten your sacch rest, boil, change your hop additions, etc. To fully automate it, you have to have the necessary instrumentation/sensors to detect fault conditions, and they're expensive. I'm not saying it isn't possible, just that it's going to be tough. Your several month timeline will be stretched to several years by the time you finish.
I'd advise you to break the project into smaller ones. Each runs to completion, then the operator (you) is alerted. You then set up the system for the next step, press go and it performs the next step. And so on. This will allow you to squash the bugs in your system in a systematic fashion and it will also allow you to make sensible changes on the fly. Once these bugs are gone, you can then look into chaining these automated tasks together, a couple at a time.
I just wanted to warn you because I've been developing products and systems for many years and nothing ever works the first time. Take it from me, your project is very ambitious.