I've been training my hyper JRT to not jump at me for attention. Rewarding and praising him when he was being good(waiting in a sit position, and remaining so when I was petting him) and ignoring him when he was pestering me for attention and/or began mouthing/licking my hands when I was petting him.

Now the progress is so astounding that I got another problem. He figured it out and he sometimes follows me around, sitting at my feet and looking at me expectantly. If I praise him, he's running the show, but if I don't, he goes back to his old habits (he'll poke me with his paw, for example).

I'm pondering two solutions:
1)Ignoring him when he comes to me for attention without my call.
2)If he comes at me for a pat, give him another command before doing so (ex: if he's in sit position, ask him to lay down, and wait a moment before petting him)

So far I've been doing combination of the two. If he rushes at me without any reason, I ignore him. When he gives up and goes away, I call him back and put him in sit+stay before I pet him.

Am I going to confuse him that way ?

I would ignore him when he approaches unsolicited. I would continue ignoring him when he begins to paw. He will learn quickly that he gets praised only when YOU solicited the contact. He does not dictate when you praise him.

Teach a "place" command.

When he gets underfoot and is being obnoxious, you can send him to his "place". Stationing a little doggie bed, or a simple mat in each room, and teaching him to go to the nearest bed/mat on command, should help.

With my dog, I used these in the rooms she is allowed in with me:
http://www.bedbathandbeyond.com/assets/product_images/380/9689914869301P.JPG

I have one sitting off to the side of the doorway in any room that she accompanies me to. A simple "go lay down" tells her to go to the mat and hang out. It lets her satisfy her urge to be close by and observe my goings-on, without having her underfoot.

The place command is a blessing.

I can't say that this is the best advice for you, and I'm partially "borrowing" someone elses thoughts on this because it fits what I like. I want my dogs to pester me for attention. I spend a lot of time training and working with them to want to engage me for everything good. I don't want to punish them and ignore them for doing just that now.

What I like about the place command Alyssa brought up is it can be something positive for your dog. My dog engages me, I praise, then I happily have him "place". My command is settle but it's for the same purpose.

Engaging you for everything good is different than constant pawing and pestering in search of treats and praises. I pictured the dog annoying the OP constantly in search of affection. I like when my dogs come up for affection, but if they demand it, they don't get it.

Wouldnt be the best advice for you either then.

Well, he's not *constantly* begging me for attention. When I do pet him, I say "ok, it's over!" in a happy tone while doing a "shoo" gesture.

I understand now it would be better to give him something to do rather than just "go away". Thanks for the advices everyone.

I often use his crate for this, but he generally just stands there looking at me, waiting/hoping to get a release command.

I presume the dog gets corrected for getting out of his mat without being asked to when given the "place" command ?

I was focusing on your second paragraph and I read it as a good behavior that I would reward. It sounded like you had solved any problems he originaly may have had and he was giving you what you were asking him for. I did correct for him getting up from settle. It may be a little different with an actual place your sending him to, I'm using it more as a casual down wherever we may be.

I usually just say, "Noooo, go lay down" when Danke leaves her mat.

Sometimes they forget after they've been there for awhile, you know?