As I see it, the "problem" you have is you have a single "input" but you need two "outputs". Like you say, the Pennsy signal has two "hot" wires. One turns on the proceed (vertical), the other turns on the slow-stop (diagonal-then-horizontal). Father knows best. The relay converts a single input into two outputs by virtue of its two contacts (aka NO, NC). So the relay sends whatever is hooked to the COMMON terminal to either the NO or NC relay output depending on the single input.
From the Custom Signal instructions for their crossing flasher:
I don't know if this is what you have but it suggests their boards even have a detector output signal which could drive an external device such as a relay. If you are using a 12V DC supply as they suggest, your problem could be solved by a 12V DC relay module you can buy on eBay for less than $2 shipped.
http://www.ebay.com/itm/1-Chan...;hash=item463288f5cc
