Okay, finally had a moment to update the post. I left out one crucial detail: Hunter is six years old.
jys1011: I feel we're getting to know each other pretty well. I spend a great deal of time with him and we're doing three a day walks(grueling at times). I'm not sure we've reached the "trust level" yet, but he responds positively to me, and he's showing a lot more character than when he first came home. It's been a short amount of time, but I feel there's progress. I also picked up some great treats that he loves, but so far it's hard for him to get used to the concept of treats as a reward. In terms of aggressiveness, he's not a biter, although he did take a good nip at me when I ran him off leash at an empty dog park. He has problems with male dogs and will show his teeth and make one of his noises. Hair raises on the back, I know it's a bad situation. He can be around other dogs, but needs his space. Also, I think people might have had the wrong impression when I said "assertions of dominance". I've watched a ton of Cesar Milan and tried some of the techniques he uses. Needless to say, I'm not pack leader yet.
Vanessa626: A gate might help, especially in defining space within the house, IE my room, his bed, etc. He's adopted a spot in each room and will go out of his way to keep it (sitting on laps, etc). I really love the breed, I had a Shep/Lab mix when I was young but mom always had cats around. I grew to like their temperament but was still a dog guy. Hunter is the perfect mix of the two.
nomrbddgs: He immediately runs from the kennel. He actually refuses to enter the room it's kept in. The time I tried to lead him near it on leash, he did a 180 and lunged so hard he was suspending himself on his hind legs. That's when we stopped with the kennel. I'm going to try to feed him there and use treats as positive reinforcement, but if he has something traumatic related to kennels I'd rather get a gate. The Cesar tips I tried were simple things like walking ahead when we were out (apparently this doesn't happen), walking out the door first, etc. He immediately runs ahead. When we're outdoors, he forgets he has a name.
Barklessdog: See, I thought I was winning him over when he started sleeping in the bed. He has a terrible habit of trying to sleep in between legs or cuddling up behind them. The crate training has been a nightmare as detailed above. I understand how feeding him last works with other dogs around, but I'm lost otherwise.
BDawg1005: Great post, thank you. After I get done with this, it's on to more crate work. I appreciate that they're smart dogs, and that nothing comes fast, so we'll continue to work together. He'll let me pet him, and scratch his belly, but he doesn't get excited. It's like he's Mr. Cool and of course I'd want to pet him, I should be so lucky! I love that about him. He pretends to be a lazy bum most of the day, sneaking off to find the occasional pen to destroy. The problem is that I spend time working on the computer in my room while he's in the living room unattended when the roommate isn't around. I need to find a solution to that. He's a big snuggler in bed and occasionally when we watch T.V. I'll make sure to get some pics up later today or tomorrow.
Quercus: I've been in regular contact with the coordinator of our local Basenji rescue (she's quite familiar with Hunter) and have e-mailed contact with several members of the local Basenji organization. Before we knew about his chip, I was trying to contact anyone who might know his owner. Honestly, I didn't want to admit to them I was having such a hard time… although, they probably know anyway! 
I'd love to get a trainer, but with all the costs (crate, food, leash, testing strips, vet fees) and then possibly getting a gate and a different leash, it's just going to have to wait.
Thanks everyone for the advice. I'll put up some pictures soon!
MHG
My little Lexi would take our Dobie any day. She always ate first and was alpha.
