Could be that or it could be from too much pressure while cranking. My old 01 did that with the fass hpfp, which is pretty much the same thing as your raptor.
The factory set up the lift pump to pump while the engine is cranking. If you have a fass or raptor or airdog, you are feeding the pump with alot more pressure than what the stock lift pump was providing. Too much pressure can sometimes cause these 24v trucks to crank for a long time before they start. The way you fix this is to find the wire that turns the pump on when you engage the starter and run it into your power window fuse. That way when you try to start the engine, the pump will not run while you are cranking. That second that the pump is not running will be enough for all that pressure to bleed back off. The pump will always be running when the key is on when you have it wired up like this.
Im not saying this is or will fix your problem, but it is something to look into. The way to tell if this is your problem is to pull the fuse on the raptor and then try to start the truck. If it fires right up with normal crank time, then this is probably your problem. The truck will start and run with the pump not running because the vp44 will siphon fuel from the tank.
For a detailed instructions on how to do this, do a search for " FASS Hard Start Fix"