The shavings in your filter are from your nearly dead lift pump, If I were you right now I'd focus on getting an upgraded fuel system installed rather than your APPS. Because if you have 10-8 psi at Idle which is bare minimum, when you push on the throttle you will prolly drop it down to near zero.
New VP-44 inj pump $1200-$1300, and that's not including labor to install it
07,5.9, 4wd Mega Cab, 3500, Dually, Auto, Rhino Liner, SMARTY CR, (Thanks To Mr. Wagner!!) Quadzilla Commander, (Diesel Nut) ICEBOX Intake w/DPP Torque Tube, Fleetguard FS20000 Lubricity adding, 5 micron Fuel Filter setup. (W/Custom made Bracket):thumbsup. SOLD