Like many I have subbed M3.5 with M4 for availability. A 4mm drill bit barley skims the plastic enlarging the hole, so all good. However I find that the nut cages that are all over the part are too large to adequately grip the standard M4 nylocs which I have? This makes it very hard to assemble as turning the bolt into the nyloc often requires considerable torque and the cages make it impossible to get a set of pliers or other tool onto the nut. Anyone encountered this problem?
I should add this is the 24.5mm version. Perhaps they were enlarged with the model when it was bumped to 25.4mm? http://i.imgur.com/H4IzJRn.jpg
Yes, it is as you have described. I’ve just used a small needle nose pliers in some of them.
Hey Jon, Yep, I had the same problem. Ryan recommends gluing the nuts in place, which is cool, and ok for him to say because he isn’t living in terror of having to undo them all again! 
I will glue mine, one day…
Meanwhile, I designed this nut encasement:
http://www.thingiverse.com/thing:1904014
which worked for me. It needs to be printed with a narrow nozzle - I used 0.25mm and they’re a pretty close fit.