pre drill your holes
counter sink the holes with a bigger drill
put a line of sikaflex on, more on the inner edge so it doesnt squeeze out the outside
put all your pop rivets in the cowl
lower the cowl down onto the bonnet using the rivets as a guide
pop them up
if sikaflex comes out, get rid of it, you cant really paint over it. well you can, but its best not to have any
then when its all cured, fill in the tops of the pop rivets. you could fill the gap between the cowl and the bonnet too if you felt like it, but i supposed it depends on what the gap looked like. if it were tight, then you probably dont need to.
the pop rivets really just keep the cowl in place while the sikaflex curesonce its dry, its not coming off.
i do this with HVAC units when i do conversions. a couple of times ive fked up and glued the box like 3mm off, and pulling it back apart nearly destroys the plastic.