davrukr - I learned a long time ago, the only stupid question is the one you don't ask.
As to your questions:
A. I try to paint as much of the interior base color as I can before assembly (even still on the sprue.
B. I rarely put tape over wheel wells and cockpit openings - it tends to lift and let overspray inside - I usually fill the opening with dampened tissue paper and remove that with tweezers when finishes - just don't try to pack it in real tight - you'll break details off.
C. I use liquid glue 95% of the time - If at all possible I try to apply glue to each side prior to putting them together - if I'm going to put the two sides together and then apply glue, I try to be vewy, vewy careful - even then I occasionly glue my fingers to the subject.
D. As far as paint schemes go, over the years I have come do distrust the manufacturers schemes. I've noticed that the patterns for paints they give are usually correct. However the colors of paint they give are very suspect. The only way to correct this is to build up yours sources. there are a lot of places on the web that will give the data you need. Check your LHS to see what they have on hand for references. Ask questions on the forum for where you can find references.
On your use of acrylics over enamels, acrylic washes shouldn,t lift enamels and enamel washes shouldn't lift enamel base coats. You should let the base coat dry for at least 24 hrs before applying the wash.
E. On painting canopy frames, to me, the best thing I've found that are the masking kits (Eduard or Magic Mask). Only problem is that they are for individual models. Bare Metal
Foil works ok but right now I prefer to spray clear decal sheet with the models base color, cut that into the proper width strips and apply.
You are probably going to get a lot of advice from your questions. For what it is worth, my advice is this: there are probable two to three different ways to do something on your models. Try the all of them and then go with the one which is comfortable to you.
What works for me may not work for you and I've yet to find any answer in modeling which is absolute. Good Luck