You guessed right on the spring arrangement. The looser coil goes on the valve and the the tighter coil goes on behind the striker.
Brass Eagle Tech Support - #1443 Raptor Silver Eagle Semi-Auto Marker (discontinued)
The spacer (part #27) is optional if you really want to make your marker shoot really really hard.
Make sure you have all the parts lined up in the valve/striker assembly.
Don't forget the valve guide (part #2, looks like a star washer) and make sure it sits square on the valve.
Also make sure that the spring guide is there (part #28, it doubles as a tool to get the connecting pin (part #6) out).
Sometimes the striker spring gets really stiff in which case you might have to do the dreaded spring cut. Just make sure you cut only 8th's of a turn off the spring before rechecking if the marker is still having your problem.
As for your velocity adjustments problems, what specifically was it? Was the speed to low or too high? Or was it just bouncing all over the place?