Hey Darwin…
Glad you liked the linoleum idea...:D:D:D
No I wasn't suggesting you use the xpen at night...I was suggesting you use the xpen during the day or when you go out :). With the litter box, my pup only has the litter box in the xpen, otherwise, there isn't another one in the house. She has never tried to go in anything that resembles one anywhere else in the house (she's pretty much house trained at this point when she is free - 100% on the poop, 99% on the pee), so I know she is not associating using the litter box with being able to poop or pee anywhere in the house. Another thing on the xpen...it helped with my girl Ruby when she was an only dog. She had separation anxiety (she was a show dog retiree and had never been an only dog). She would pee in her crate from nerves...only when I first left. Once I switched her to an xpen and crate, she had more room and was much better about being left alone and never peed again in her crate (or the xpen). I know peeing is not your issue, but it is the same sort of nervous reaction. But that is what works for me, the xpen was just a suggestion and wanted you to hear a few examples of how it works.
It might be your pup has separation anxiety, especially if he won't eat when you leave him a treat like bacon. From a suggestion on this forum, I got a snuggle puppy for my pup's crate...a stuffed dog that has a heart that emits a heartbeat and heat packs to keep the body warm...so it resembles having a litter mate. Do a search on the forum for another thread on that...has a link to where to buy it. Another thought is Comfort Zone (dog pheromone)...comes in spray or plug-in form, available at most pet stores or online (coupons are on their website)...some people have great success with it, and I would think it might work better on a pup that left its siblings as early as yours did.
Another thing that might help, try to make sure your pup is really tired when you leave. He'll might be too tired to notice you leave.
I'm plumb out of suggestions...maybe someone else will chime in. And remember, rational for a puppy is probably not what you or I consider rational at all...ha, ha :D.