Jorge,
It may be that a couple photos would help to get an accurate read on your problem. I say this because I did not have the same issue. The 4-4 size was just right for the 8 rivets joining W-1216-L&R (14-02, Step 5 & 6). As noted (several times it seems) by rgmwa, Van's should help you make the ultimate determination.
If you do need to drill out any, it should be plenty easy enough. One of the principal skills I have been developing in the course of my project is that of drilling out rivets. I'm getting pretty good at it if I do say so myself. If you've made it this far without having to drill out a bunch, you're doing very well.
I would like to wave a yellow flag about the next step, though. In assembling the inboard hinge bracket (Steps 7 through 10), the instructions say to use AN426AD4-6 rivets in the two locations where they're required to be flush on both sides. These rivets are definitely too long for that application. This was later confirmed to me by the factory. If you use 4-6, you will either have the shop heads protruding, or if you set them hard enough to get them flush, the bracket will be distorted. Use AN426AD4-5 instead. Here's the catch: there are no 4-5s included in the kit. If you don't have any of that size already, you'll need to get a few.
Happy squeezing.