I don't fully understand your requirements, but can you just join the two boards together using an Ethernet switch? That would probably work the best. There are usually 3 issues joining two boards together as you've suggested...
1) Power problems - make sure you have a good solid ground connection between the boards - you can measure ground bounce between the boards by grounding a scope probe on board A and measuring the ground on board B.
2) Signal Integrity - make sure your signals are terminated correctly, in particular the clock or latch signals. If you have reflections on a clock or latch, the thing won't work no matter how slow it runs. You can also mess with the slew rate and drive strength settings in Quartus.
3) Timing problems - I'm assuming you're using a synchronous interface (clock and data). On the transmitter, two techniques help here... a) Use of I/O flip-flops and b) treating the output clock as an additional data pin. If both clock and data are generated by the I/O flops, they will all effectively have equal skew. On the receive side, you should consider sampling the data on the opposite edge of the transmit clock ie sample the data in the middle not at the transitions. You should also look at the DQ/DQS structures on Stratix. They provide a dedicated structure for clocking/latching external signals, but you might not have access to them on the Stratix Board.
High speed serial is not a good choice unless you have a proper connecter and routing scheme. If the 1S40 board is similar to my 1S10 board, this is not the case.
Good luck, John