Matt,
its kind of a catch 22, Its sure easier to spray the clear on a complete airplane, but its really hard to get decent, if any , coverage between things without a gap of 1/4 inch or so, even then, its pretty iffy.
I spray everything in pieces. See pictures Randy has posted about how he holds flaps and such. the motivation to spray it assembled is pretty clear when shooting and masking colors, but you can hold it together with brass strips instead of hinges when you are masking color. Its actually easier than hinges for that purpose. Then yank that bad boy apart when you shoot clear, I even clear it with hatches removed and held onto small paintsticks.
Omni is decent clear, its a bit more Acrylic than 2024 which is what I typically spray.Acrylic makes the clear much more user friendly when spraying and polishing. The 2024 is higher in crosslink concentration, more Urethane,, Its a bit stronger chemically and I beleive higher in UV filters as well.
Nothing wrong with Omni at all.
Might I suggest after the repair, you then coat the inside of the cowl with epoxy, or clear ( since its been exposed to fuel, epoxy may be a better choice) make sure the inside clear/epoxy overlaps the edge of the clear on the outside of hte plane,, to protect the edge. For what its worth, when I spray a plane in parts, most times I can clear inside the cowl at the same time, or I will spray the inside, let it dry, then spray the outside as well.