So I got out to get on my bike this morning and the fender under the tail section was sitting on my tire. After closer is looks like there are two bolts, one on either side. Both of these bolts are missing. Does anybody know what size they are?  I'm not sure what size they are.

Looks like there are 5 bolts. One in the front, 2 in the back, and 2 in the middle, if you mean the 2 in the back they seem to be 6x16 mm according to fiche:

http://www.ronayers.com/fiche/300_0284/rear_fender_model_y/rear_fender_model_y.cfm?man=su&groupid=3160&parent=3070

Ya the only bolt that i have out of those five is the one in the front. So now all i need is the size in the middle,

i've had to tighten the 2 back bolts twice, keep an eye on those/all bolts