Well I've screwed this up something proper. I would love to be driving an extremely underpowered 4 banger right now. I've crossed the 6 month mark in what was supposed to be a 3 month process. I've yet to add up the cost, but it'd be safe to say I'm over budget as well. My wife is an awesome an very supportive woman.
The gents at the shop who were "fixing the slave cylinder" for me found play in the throw out (TO) bearing, brought it to my attention, and I agreed that them removing the trans to inspect internals was the best course of action.
Unfortunately, I'm real busy at work and don't have time to do this myself, but more than that, the guys doing the work are a lot more experienced than me so I trust that I'm getting the work done rioght, and honestly, it's not taking any longer than if I were doing it.
Upon removal, they found that I used some wrong parts when installing the clutch & TO bearing and apparently pushed the TO bearing through the front of the trans.
Clutch it toast, TO bearing is wasted, front of the trans is jacked.
To say I was having trouble with the slave cylinder was understatement of the year.
The trans would need 300-400 worth of rebuild for it to be useable. But, it came free with the Atlas, and who knows what the condition of the rest of it is. Rather than spend money rebuilding part of that trans, I ordered a new rebuilt aluminum top SM465 from Midwest Trans, it ships Monday 6/30.
The shop agreed this to be the best course of action, and offered the same labor cost for removal & install, so I'm really only out a few hundred more for a completely new trans with warranty.
Again, to say I screwed up would be quite the understatement. It is good to know now what the issue is and be moving forward. I can certainly say, that if/when I build my late 60s longbed Ford pickup that I will most certainly use a motor & trans from the same vehicle. Combining a motor/trans/case from 3 different sources is just asking for trouble, especially considering this is my first motor swap.
Living & learning.