Thank you all for your input. I want to address some of the things that were said here.
First off, I think we should encourage people to discuss mistakes that have been made even if it is "Greg Hiller" we're talking about.

For two reasons. First, even he can make a mistake or not think of something. And second, others reading it can learn from it even if the person in the specific situation already knows. When I'm having a problem, I always appreciate any thoughts people have on a subject. (Ok, so that was kind of three reasons)
That said, let me provide some more details.
I normally do not do such a long acclimation. However, I don't think such a thing will cause a problem.
The acclimation was so long mostly because I intended to quarantine the clam for several days. I have clams in my tank already and I didn't want to jeopardize them.
My biggest mistake, IMO was putting this clam in my tank. That act violated the whole point of the quarantine and in hindsight was a stupid thing to do. When I saw it going downhill I reacted rather than thinking it through (and posting here for others thoughts).
For those that were concerned about the long acclimation and O2, an airstone was used due to the fact that I knew the clam would be in Q for a few days.
Again in hindsight I think shipping stress was the cause. The package was well packed, properly marked and the appropriate pleas for gentle handling and "this side up" were present, however it still was leaking when it arrived. The type of packaging used had to have been badly abused for the exterior packaging to get wet.
All the signs from the first time I saw the clam were bad. I just didn't want them to be true so I ignored them. I think this is a mistake we probably make more times than we want to admit.
I hope this situation can be a learning experience for somebody.

I haven't lost something in a very long time. It never gets easy. Sorry it had to be your clam zenya.
