Right now it relies on 4 temperature sensors and two controllers with four relays each. Only six of those eight are being used. Those controllers handle multiple RIP relays which in turn shuts pumps on or off.
A few more input sensors might be nice and at least the eight outputs I have maybe more.
A couple years ago I bought the Arduino Duemilanove to play with and see if it was something I could use but I got busy and never got back to it. Now I see the Duemilanove is not produced anymore.
Any advice would be greatly appreciated.
The Duemilanove is still supported by the current arduino IDE and will run all the same sketches and library code that the current Uno board does that is based on the identical 328p micro chip. So your Duem... board is as relevant and useful as the day your bought it.
As far as your boiler controls go, there are very significant safety aspects that go along with boilers, many are defined and enforced by law. You need to clearly understand what sensors and controls are safety related and that should be independent from any controller you use to run the boiler. This in not a trivial or simple project to take on and dependent on your specific knowledge and experience may not be a good arduino project to take on. If the boiler is operational already maybe just have the arduino be a boiler monitor and data collection device, rather then actually controlling the boiler?