I’ve read that Paint as many Parts on the sprue as possiable but when that is done when it comes time to glue them together does the areas that have to be joined have to have the Paint scraped away?or because of CA Glue can they joined without Scraping?
If you do paint on the spru you will have to make sure there is no paint where the glue will go. Even if you use CA glue it will stick but the paint may not 
So scrape before painting.
The issue is not the CA to paint bond. CA glue will stick fine to a painted surface. The real question is whether the paint under the CA glue is bonded well enough to the surface underneath to hold on the part. If the joint fails, it will fail bewteen the part and the paint rather than between the CA and the paint. It’s always better to scrape paint down to plastic where the parts join, but in some cases you may be not be able to do that, and depending on the exact nature of the joint, it may be OK. Use good judgement.
I’ve tried that and didn’t had good results. I prefer to paint subassemblies. For armor, I paint the wheels, track and pioneer tools separately then I paint the complete hull and turret before attaching the wheels, track and tools on it.
For aircraft, wheels wells, landing gears and cockpit is painted seperately in sub assemblies and then masked when ready to paint the whole plane.
[#ditto] I agree with Yann . All of the handling during assembly ( glueing , puttying , test fitting ) will ruin your paint job and make assembly more difficult , IMO. Good luck .
Same as Yann above, I paint in subassemblies. However I do sometimes paint parts on their spure, but very infrequently. The later is really a matter of personal preference, but like already stated, carefully sand/ or scrap the mating surfaces where the parts are to be joined for the strongest possible bond. Also worth mentioning, use a minimal amount of CA for the application to avoid excess “seep out” from under the joint.
For ships i tend to prime on the spur and touch up if needed. The primer will increase the dry time of the glue (i use model master: liquid cement), but it bonds just as good as if there was no paint. No problems with super glue.
As for priming everything else, I rarely prime on the spur tree. I assemble everything untill it is all ready to be painted, i then prime all sub sections and individual parts.
For small parts i use strips of painters green or blue tape turned upside down and itself taped at the ends to a piece of cardboard, this will keep them from moving. I use a spray can to prime (Here is a link to a post that i made on my favorite primer), i spray outside due to fumes, i also took a cardboard box and cut away the the top and one side to make a wind break.
I never paint on the spur, but this is mostly a lack of forsight as some parts that i would paint by itself have the spur tree attached to a non visable area.