I have a 5.4L, 4.10 gears with factory LS rear (9.75) and Eaton front LS. I had stock 3.55's. Before getting blown, I wished I'd gone to 4.30, even with a 5.4L. If you're going through the expense of a gear swap, I'd do the 4.10, especially with the 4.6L. This gearing hits the sweet spot of the power band, and does not noticably affect gas milage. You will, however need a chip to correct the speedo / odometer for the new gear ratio difference.
In my opinion the expy should have had 4.10 as an option.
But than thats only my .02c !