One other thought...how did you set the preload on the pinion when you changed the pinion flange? Did you use a new crush sleeve? If the pinion preload isn't correct or the pinion nut has come loose it could cause some clunking noise.
Make sure your axle nuts are tight. Loose hubs can cause the symptoms you described. Add friction modifier. Did you use 14mm or 9/16" bolts in the front subframe bushings? If not you may have movement there making the clunking noises.
They're still out there. I bought an M58 new in the box from a Ford mechanic in VA last Nov for $360. It popped up on Craigslist. Box was a little worse for wear but the M58 was complete with clamps and the the tailpipes were still wrapped in the foam shipping material.