Possible reasons why your lamination was inconsistent:
- Skin was taken out of the fridge too early (or put in too late). If you let a laminated skin warm at all before topping and baking, there's a chance the layers could merge together and become more like a single-layered skin.
- Baking temperature. 400 is very low. To me that's not even baking; it's more like warming. With that low of a temperature, instead of actually baking the skin, the first few minutes of baking could simulate proofing. If so, then that could be just like letting the skin warm up, which likely creates a situation very similar to my first bullet point. (I don't know, though, because I've never baked a pizza at that low of a temperature.)
- Screen. Especially when combined with the low baking temperature, baking on a screen might create conditions not unlike proofing for several minutes, which could make the skin's layers merge.
- How you rolled the skin. One thing I do before folding and laminating my dough for this kind of skin is roll it as thin as possible; much thinner than a sheeter could roll it. (I think I actually got this idea from one of Dan's posts from several years ago.) Not only does this make it easier to roll the dough after you fold it, but it also seems to create a more ideal crust than if you don't do it this way.
- Too much yeast. 3% IDY is a ton of yeast. As long as you're not overfermenting your dough (which you very well may be doing, considering your dough's high yeast percentage AND the long room-temperature bulk-ferment), excessive yeast is probably one of the reasons why you don't end up with the laminated texture you seek. That is, if the yeast is still alive and working by the time you roll a skin, it's gonna keep working at a very fast rate, which probably makes the layers merge, just like if you put the skin in a proofer; even at cold temperatures.
My experience says rolling by hand can achieve the same results as rolling with a sheeter. (It just takes a lot more work.) And having baked two nearly identical laminated pizzas a week ago (one I rolled by hand and one I rolled with member waltertore's sheeter), I am even more convinced that what I just said is true, because I couldn't tell any difference between the hand-rolled pizza and the sheeted pizza. By the time the two pizzas were cut and served, I had lost track of which was which, and I wouldn't have been able to identify which was which based on how they turned out. The only procedural differences between these two pizzas were: 1) One was sheeted while the other was hand-rolled; and 2) The skin I rolled by hand was rolled about 16 hours earlier than the skin I rolled with the sheeter.
Rather than baking at a lower temperature in response to the toppings not getting done, I'd crank the oven all the way up, stop using the screen, and instead peel the topped skin directly onto the stone. In fact, that's almost exactly what I've done with my own laminated pizzas, except I used to bake my laminated pizzas on a perforated pan, rather than on a screen. As far as I'm concerned, screens are useless except when used as makeshift cooling racks. Screens are for beginners and people/organizations who value ease and convenience over quality (like Domino's). Unless you're baking in a conveyor oven, a screen is nothing but an obstacle between your pizza and the heat/thermal mass that's supposed to bake the pizza. There's essentially no point in using a stone to bake a pizza if you put a barrier between the pizza and the stone's heat (unless the style of pizza you're baking requires a pan to keep the pizza's shape).
I know all about sharing pictures that are not necessarily representative of the entire pizza. Most of my Tommy's pics are from pizzas like that. Not anymore, though. As of summer 2013, I don't have to be picky when sharing pics of my Tommy's clones, and I really make no effort to take good pictures. Pretty much every pic is representative of the entire pizza. I didn't even take pictures of the pizzas I made in Walter's classroom because both of the pizzas looked just like the most recent pictures I've shared (regarding the lamination, anyway).
If you increase the yeast, it will likely only take you in the wrong direction. If I was you, I'd start by cutting the yeast in half. The long room-temperature bulk-ferment, especially in conjunction with that much yeast, screams "overfermented" to me. (That probably doesn't really affect the issues you're having with lamination, though.)