The ACC system (used from '83-'87) uses a mix of vacuum controls and electronic brains. Needless to say, a disconnected vacuum line can cause a lot of problems and unusual operation, and they're easy to disrupt when changing a heater core.

I wouls start by checking the vacuum connections at the coolant control valve to the heater core. It's in the engine bay, right against the firewall, mounted inline with one of the heater hoses. Also, check the bundle of vaccum lines where it passes through the firewall (a few inches away). Check as many of the connections as you can inside the car (without dismantling the entire dash), and pull the ACC head unit and check the bundle of vacuum lines entering it from the back. If you are still having issues, it may be worth getting an "Interior & Climate Control" service book off eBay. If you can't find one, email me directly (click on my name or the mailbox next to it at the top of this post).

God bless,
Fitz Fitzgerald.
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'87 Blue 240 Wagon, 254k miles.
'88 Black 780, PRV-6, 146k miles.