Bit late to the party but mine is setup the say way you described in your first post, you need to have it tuned to work with the AFM in that position. I can guarantee the way you have the AFM setup in that pic will give you boost leaks, you have chop it up and install into an ally or steel pipe.
Also the oil feed on the turbo should be vertical if possible. Coil packs look stock too? If they are the originals then you will need new ones or you wont make it past 10psi without a miss. Your gonna max out those 555cc injectors pretty quickly too, < 300kw.