Normally I use risers to get the puppeteers higher but for the program we will be doing, I have two out of four who are short and need to be higher; however there is A LOT of walking around that makes it impossible to have risers behind the stage.

Is there something I can use to duct tape to the puppeteers feet that will give them the height and walking ability they need?

Why not look at what the bunraku performers use? They're a type of platform shoes. See the second-last picture here:
http://www.puppetsinmelbourne.com.au/faq.php/2010/05/17/training-with-ningyo-joruri-bunraku-behi

How about a classic?  Try paint cans.  Hot glueing something grippy to the bottom is probably a good idea.  Or you might consider some of these:
http://www.stiltman.com/html/stilt_plans.html
 

Wouldn't stilts be awfully difficult to use? I mean, I know they're used a lot for puppetry in terms of costuming (ie Landstriders in The Dark Crystal, The Lion King), but combining 'normal' puppetry - moving rods, pulling strings, etc - and stilts seems extremely difficult to me.

But then, I've only been on a pair once in my life, and that was tricky just keeping balance

Why not make the tall folks adjust.   I am not sure what the difference is in height, but I often preformed with a shorter partner. First of our main playing area was normally lower and we had rolling stools that we sat on to preform here. That is pretty easy to adjust since mine was lower then hers. We did have an upper back playing area on many shows, but there I just bent over a bit to preform.

My husband actually made a pair of "buskin" type shoes for one of our small puppeteers - he fastened an old pair of her slip on shoes on to styrofoam blocks and she is able to walk around quite easily when she needs to. If she is moving from the front tier to back stage one of our other puppeteers helps her slip into them and off she goes. I will see if I can take a picture.  We do keep the stage as low as possible too but she happens to be one of our best puppeteers and is just tiny, so we had to do something.

We have many different risers and some of them are actually wooden platforms about 12-15" wide and different lengths. We can put them on floor behind the 2nd level of the stage, stacking them if need be.
Our lower level is for kneeling, (platforms can be used here as well), 2nd level for standing. Our puppeteers range from 5' to 6'1".   

i agree, make your taller puppeteers adjust

Ideally you want to raise up your shorter puppeteers using some kind of platform shoe (like Na suggested). Television puppeteers do this, you can usually have a cobbler make a custom platform shoe if need be. That is the best and most flexible solution.

Having taller puppeteers crouch or adjust their height seems like an easier solution, but I think it's a bad idea from a health and safety point of view. I've certainly had to duck or crouch to accommodate shorter puppeteers (I'm about 6'1 tall), but you can injure your back (which I've also done more than once) that way and it will create unnecessary physical strain during a live show that lasts 20, 30 or even 60 minutes.

At work we use a variety of things to even out puppeteer heights without special shoes. Here's an example -

MsPuppet's riser system sounds interesting too.

have you ever used "risers"   models use them to make them look higher in their high heels. its a small wedge that goes in the back of your shoe. they are really uncomfortabe but they do the job. i made some out of duct tape fabric and cardbord once and it gave me about an 1 1/2.