******** UPDATE *****************
So, I've decided to hold off on the Tufts evaluation, due to cost, and in speaking with a trainer I have worked with (who unfortunately doesn't live near me any longer) she has known people to go there and come out with pretty generic information and/ or a prozac prescription for the dog!
I've been diligent about striving towards being the pack leader, though it has not been without it's challenges.
The first week or so we had Cerbie in the crate at night in the basement, he whined and moaned throughout the night, keeping me awake. In the past, we had automatically assumed it was due to his leg discomfort, and had let him out and stopped the crating. It killed me to keep him in there and ignore him, but his protests have stopped. It is a large crate, so there really shouldn't be any pain issues.
For the first couple weeks he seemed really depressed and lethargic. I'm usually the "softy" who caves when I see this happen, but I've been committed to this, so I've remained strong. Lately, he's a wiggly happy boy when let out of his crate in the morning, even my s.o. has noticed a change. He's been much more obedient (even around the neighbor's cat when off leash. He attempted to break his down, but one stern voice correction fixed it and he was calm again, even as the cat approached and was pet by us.) He still tests us, and I think he always will, but I have great hopes if we remain strong and committed he'll do fine.
I've started implementing marker training, though I have some questions and have yet to get my "basic dog obedience" dvd working (operator inadequacy with mechanical devices!) I've been more consistent with training, and I see that it's paying off! We've even recently taught him to "play dead", a wonderful calm submissive posture. I have to work on the s.o. also, as he'll have Cerbie "play dead" and approach him to pet him, thinking he's getting him used to being pet. I've just reinforced we have to be working on training him, becoming pack leaders, and building his trust, without forcing things he doesn't like (like being pet when laying down.) I think that's the hardest part of all of this: trying to convice a human when their thinking is not in line with nature's principles!
There have been no aggressive reactions recently. He's being fed in the basement, and I have him exercise (work for his food) then sit and make eye contact with me before being released to eat in private. I'm not feeding in the crate, but there's a corner of the basement we've made a safe place for him. Initially he'd wait for me to walk away and up the stairs, but now he'll start eatting immediately upon release, definately not as threatened.
I'll tell you, dog training is definately not an innate thing to many of us. I personally was brought up to expect a lovey dovey snuggly dog, but I realize now this is a stupid and dangerous expectation. Thanks to everyone and your replies! This is one site I make sure to visit to continue my education whenever I have time!