I'm not that up-to-date on front overhauls, but I'd guess it's the tie rods. If you didn't replace the suspension arms, the ball joints have moved to a new position due to the lower springs and may be giving you that thumping.
Did you replace the rubber insulators on the coil springs? How did the top "hat" bearings feel? Are you sure both the new tie rods have good joints? It's not impossible that one is bad. What brand did you buy? I had a bad joint on a brand new suspension arm from FCP Groton once.