Misfire on Cylinders 1 & 5
 

2005 S40 2.4i (B5244S4) - just rebuilt the motor in this car and started it for the first time. It was running rough, and needed to be revved to stay running (otherwise it would sputter and die). It's throwing a P0300 (random/multiple cylinder misfire), but no other codes. After checking and swapping around the plugs & coils, and checking the wires, we determined that problem is specific to cylinders 1 and 5, and all the plugs, coils, and wires are fine. What should be my next step here?

Are the cylinders firing at all? I would run a quick compression test on all cylinders just to verify everything is the same. After that I would check the spark plug colors to see if those cylinder's plugs look lean or rich. If the car sat for a long time the injectors may be clogged with old fuel.

Why did you rebuild the motor? If it was because of a broken / slipped timing belt, I'd suspect valve damage to those cylinders. The compression test Hudini suggested will confirm that hypothesis...