Thanks for getting in touch.
I think I get the jist of your problems and how to solve them. Have you just made the transition to a shortboard?
There are 2 things that I think will help you and get you up in the right position and take the focus off of your toes during the pop up.
1. Start doing a few burpees ( http://www.youtube.com/watch?v=_2cPYR0lRUE
just in case) every day which should build the explosiveness and power needed to get your arms and upper body to carry your lower body up and through to you standing position. You should and will get to the point where the action comes without. Remember during the pop-up you are using your arms, upper-body to bring your legs into position in almost one fluid movement. This will take the emphasis of using your toes away. I hope this sorts that problem out.
2. For the foot positioning problem, when I am trying to lock down the right position for my feet on a board, I take off all the wax off my board and depending if I have a traction pad or not, put only a small strip of wax in the exact places both feet should be and then just go surfing to dial it in, if I don't get it right I wipe-out (safely of course).
You should try this method before each surf on land first to get the feeling in your feet for landing on the wax (or not if you don't land on it), then get in the water. Just remember when you are wiping out to cover your head with both hands and roll back if you can.
Please let me know how it goes and if I answered your question properly, if you need any more help give me a shout.
Have a good one and I hope there's a bit of swell out there this weekend for you to practice.