The first thing I want to say is - congratulations on your determination to breastfeed your baby.
Secondly, from the information you've given, I would have to say that the nipple shields are causing your problem. There is reduced flow of the milk to the baby with them. And since your baby has learned to nurse WITH them, she isn't learning how to latch properly to your breast, so trying to go without the shield will be more painful. A nipple shield may seem like a good idea to eliminate the pain, but unless the baby learns a good latch, the pain will continue.
Another thing I want to make sure to point out is, most every baby, satisfied or not, will take a bottle after nursing. A bottlefed baby will also continue to eat after it is full. It is generally because drinking from a bottle is so much easier than nursing - there is NO work involved. So the amount a baby will take from a a bottle after nursing is no real indication of hunger.
My recommendations, while they may not necessarily be comfortable, would be to eliminate the nipple shields and the clock from the equation. At first, trying to nurse before she gets too hungry will help with working on the latch. The hungrier she is, the faster she'll get frustrated trying to latch properly (and painlessly) and the fussier she will become. And don't worry about how long she is at the breast. Babies stop nursing when they're full (unlike with a bottle, where it is easy to overfed). Sure, there are babies who like to nurse for comfort, and in the beginning (once your pain issues are gone) that is a good thing. The more time she stays at the breast - the better your milk supply will be, and the less you'll worry about her losing weight.
A couple more things that may help you feel better. A baby eating every 3-4 hours is perfectly normal. The quick way to tell if your diet is an issue is more her discomfort in-between feedings.
As for weaning from the shields, she needs to learn a proper latch. Make sure her mouth is open wide before she latches, and that her lips are spread.
There are some good pictures at http://www.breastfeeding.com/helpme/helpme_images_latchon...
and more good information on weaning from a nipple shield at
http://www.kellymom.com/bf/concerns/baby/wean-shield.html.
I am a certified breastfeeding counselor, and have nursed 7 of my own children. I also have a site called BeyondPregnancy.com, so I have a wealth of links and info on breastfeeding. If I can be of any more help, just let me know.
M. J
mom to 7 great kids from 2-17