On the left side, above the cabling - looks like one piece of glass isn't touching a frame. Depending on the direction you're moving, that may be the problem. Also, I don't think you need panels for the MFSU or they cabling; they're standalone blocks that don't require a surface.
Max link size shouldn't be too large of a problem unless you try to, say, move the entire chunk. That would be bad.
Also, it may be easier to update to a 1.5.2 pack and manually add Redstone In Motion - the platform carriages would probably work well here. Just make sure you don't let the spaceship touch something like the ground or you're in trouble.