Proper glue technique

Everyone has their own way of doing things. In regards to cockpits, I glue everything I can and paint later, with pe belts added last. Since discovering Plast I Weld and the Touch n Flow applicator, it has become my go to gluing arsenal. For pe I use thick ca or Aleen's fast grab tacky glue and for clear parts clear parts cement. Any residue that manages to show up will be dulled over with a light dusting of clear flat from my AB or small brush.

I use Micro Krystal clear to glue painted parts on.  It has very good adhesion although not as good as CA or styrene cement.  Its good for clear parts, too!  I glued a canopy on with Krystal clear that I later had to remove.  I was very surprised at the amount of effort it took to pull it off.

I've also used Abtielung liquid mask to attach parts.  Its just like rubber cement but a little thinner.  And whats great about it is that if you mess it up you just pull the part off and peel off the mask.  Easy as pie.

For me, it depends.  If possible, I'll attach things before painting, but that typically is what I do for larger assemblies.  For a cockpit, I'll reverse that and paint pieces, then assemble.  I use a Nr 11 X-Acto, a straight pin or sewing needle, to remove paint as necessary.  As Don noted, CA glue is plenty strong.  After either method, I touch up as necessary.

For small parts with paint on a gluing area, I either scrape the gluing surface with a #11 Xacto blade, or use a small drill and pinvise to drill a couple of holes through the paint.  For small parts CA is  strong enough that even the dimples from a couple of small drill holes will hold well enough.

I find it a lot harder to mask and paint areas after the parts are glued together, so I am with the OP in painting cockpit areas and then gluing assembly together, but you do need to remove glue.

The only thing I glue on a cockpit after painting is color PE seat belts if I'm using them. Just have to be real careful not to leave a super glue smudge mark. Some parts such as gear doors and actuators need to be attached after painting. Again, just be careful. As Bronto said, glue all that you can together fist, then paint.

It's simple.  Glue the parts together BEFORE they are painted.  No touch up needed.