I think you are pushing too hard with the sponge applicator and using too much polish. I just did my Merlot McCallisters the other night... I basically squeeze the polish out until it reaches the end of the sponge... not to the point where it pours out, just to where it reached the end of the sponge.
On the flat surfaces of the shoe (vamp, quarters, and foxing) I will push the sponge firmly to get a little polish on that area, and then lightly spread it along the remaining parts of the shoe. I gradually put the sponge harder since I literally only use the amount of polish that fills the "hole" in the sponge. If it is really an issue, save the toe box and the broguing for the end. By that time, the sponge should be well "dampened" with polish, and there will be enough where you can apply it properly without having to add much pressure. In addition, it won't hurt to have a folded piece of paper towel that is wet. If the polish is going on too thick, you can always dab the sponge lightly on the papertowel to loosen things up a bit, however I have yet to do this. Last resort, don't use the sponge. Squeeze the polish out on to a cotton ball. Do the flat/unbrogued areas first, then the residual on the cotton ball can easily be spread across the broguing and toe box.
One thing I will always always do, is spray some water on my clean horsehair brush when I am doing the final buffing. The little trace of water will help distribute the polish evenly across the leather, can help lift up those little clumps in the broguing, and will help add a bit more brilliance to that shine.