Update: It's fixed. The clunks are gone. The culprit was dried up grease inside the steering column, on the steering column mount, and inside the steering column bearing. I discounted the steering rack, subframe mount and control arm theories because the clunks were not felt at the moment when engin...

Those bolts look vaguely familiar..... By any chance, do you still need to install the belt guard that goes around the bottom of the crankshaft pulley? It seems to me that those bolts are similar. IIRC the long nose helps get things lined up and the threads started. (Although I still found it a kind...