Hi Mark,

Your clunk sounds like torque rod bushings the way you describe it. If it matters not how hard you're out of the hole, it might be the trailing arm bushings. If you've got urethane all around maybe you can double check to see if they are surviving in place. If not that, look to see if you can tighten the shock, bar, or TAB bolts.

The disconnect into second gear, well, that, in my mind, has to be one of two things. Either your clutch or the OD. I've not had either experience, but if you think it doesn't feel like the clutch, I'd guess the OD. There are only three friction connections between your motor and the road, and I'd bet you'd know if the tire was slipping.
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Art Benstein near Baltimore

By all means, marry. If you get a good wife, you'll become happy; if you get a bad one, you'll become a philosopher. - Socrates