Here's a couple of suggestions to read, think over and use if you think it might work for you and your dog:
For starters, he's linking you to making him do things he dislikes and you probably don't like doing them much either. Maybe try getting very upbeat when you pen him - get really excited and happy, clap your hands, laugh and smile, and use the old "You Won The Prize!" anti-dog-barking technique to make it a happy time for him when he goes into the pen or goes to the vet, has his mouth cleaned of bits of things, nails done, bath, etc.
Make it hugely fun for him - dogs get excited and happy when we do - just fake it! Become a cheerleader! Cheerleaers may be breaking up with the star quarterback and their parents divorcing but there they are out on the football field cheering, clapping, jumping around wildly, whipping up enthusiasm, so you can, too! Make it believable - laugh, smile, act silly when you do the things he hates. He'll come to look at them differently. Dogs can't read us as readily as we think apparently because I can excite Tibbe greatly when doing things I just hate doing by acting happy and excited!
I hated doing Tibbe's toenails and so did he. Finally, I started calling his Gentle Paws machine a "Treat Machine", saying it's "Treat Machine Time!", while laughing, clapping, acting so excited and happy and he came to run to me after a while. He'd get his treat, we'd get his toenails done - which he still didn't love that much(because I hate it!) but at least now we're both in a much better frame of mind when we start it and finish and he's treated before and after and we both act happy about it.
Ask your family to put him in the pen the normal way whereas you are crazily happy, upbeat and smiling when he goes in. Toss in a small piece of luscious chicken or turkey hot dog, peanut butter in a kong every time you pen him or anytime possible when you something he doesn't like. I'd also try putting him in the pen for very short two-minute periods acting all happy and upbeat several times during the weekend and evenings when the family is home for a couple of weeks - you doing it all upbeat as if the dog just won the lottery and asking the others to just do it in the routine way.
Smiling, laughing, acting as if ya'll had just won a trip around the world on a luxury cruiser and inherited a billion. "Yahoo - Oh, BOY! Yes, yes, yes!!!! Time for the PEN! Yea! Yessssirreeeee!!!! Wahoo!!!!" Get really silly happy, handclapping, smiling at him as you go to lift him, laughing out loud. Keep up the happy banter all the way until he's penned and the kong tossed in and you walk away.
He'll have his kong(s) to keep him busy for up to 45 minutes when you go to work as you can feed him his breakfast in a series of kong toys, placing a portion of his food in each of several kongs. I usually feed Tibbe at least one of his daily meals in his kong toys and he loves working to get his dinner! He'll chose three kongs over a bowl of food anyday, given a choice!
Try to let up on the discipline and just use obedience training x3 minutes x2 or 3 daily working in an upbeat, happy manner training him to learn how to do obedience such as come, sit, stay, lie down, leave it, stop, bark on command, quieten on command, etc. He'll love the training if you give him loads of positive reinforcement when he gets it right and he'll begin to bond with you, respect you and look to you as a benevolent pack leader. Be confident, firm, matter-of-fact and upbeat/happy during the training - no military tones of voice but giving his commands in an upbeat voice, making him love the learning, eager for the work and the result of it - his "paycheck" - a treat and your smiling praise when he does it right. In time, and it will take some time for him to learn the "new you", you two will be a real team, firmly in love again.
Play hard to get - make him seek you out for the next few weeks. Don't initiate snuggling, kisses, picking him up unless necessary, etc. He needs to want to approach you and if you'll just ignore him for a while as you try these other things, he should begin to wonder why you are suddenly somewhat different, aloof and as soon as he begins to see a pattern of that, he will begin to approach you for affection.
ClickerSolutions Training Articles -- "You Won the Prize!"