Tom,
For the VariEze, cowl installation is covered in detail in Section II A, Step 15, and that's the method that I used. Note that there are 'screwless approaches' like Bill James, Klaus and others have used; and there is the camlock approach discussed by Joe under the earlier "Engine cowlings screws..." topic. There are several good ways to skin this cat.
So, the plans recommendation is for non-structural 10x32 machine screws, the old AN 507, used in conjunction with an appropriate anchor nut, like the K1000-3. The current screw numbers are: MS24693-S273 for the longer screws (5/8th inch total length) that I use where the spar & firewall flange is thick, and the shorter MS24693-S272 (1/2") everywhere else. The anchor nuts are pop riveted in place using the appropriate, small size that the plans give as Avex 1604-0412 or Cherry MSC 43. These are flush head and you want to countersink them in the glass. I don't know anything about bonding nutplates? Just be sure that there is no chance that a nutplate could spin on you or you'd be stuck drilling out the screw (if it didn't spin too).
The stronger AN 509 structural machine screws are not needed in this application, and I would have a concern (but no real data) that they would be prone to wearing out self-locking anchor nuts. I've also heard that stainless screws are prone to galling and screwing up the nutplates. You don't want to have to change out nutplates if you don't need too! I've had my cowl off hundreds of times using the 507s and the nutplates are still in excellent shape - none replaced!
A drop of oil on a new screw probably helps as my self-locking nut plates are still pretty stiff for a new screw. I probably get 6-8 shots out of a screw before I toss it. These days I throw away sooner rather than later, stripping out the head is no fun to deal with and screws are essentially free.
I use Tinerman washers under all leading edges of the cowl (spar flange and firewall flange). I've had good luck just going with just screws everywhere else, but you have to be sure that the cowl has plenty of beef where the screws seat, because cowl security is a serious flight safety issue, to be sure. Carefully monitor the condition of the cowl, screws and nutplates to be double sure that everything is, and stays, OK.