yes, your intake is a limtation...it belongs on a 318 not a 408.
you can not use stock 340 pistons in a 408..due to the longer stroke the compression height of the piston must change...the compression height is the center of the wrist pin to the top of the pistons...
the 340 has a CH of 1.84 inches....4 inch stroker pistons are generally around 1.45...
a 340 piston in the stroker would hit the cylinder head....
the scat 9000 is a cast crank .......if you use ebay for pricing they are selling for around 265 bucks....