Chipping agents won't make much difference however the intensity by which you 'go at' the kit matters. If you add water over your chipping layer, let it soak in and then chip away with an old brush or sharp toothpick you'll be ok but if you really go nuts with a toothpick you might scratch into the primer. Just use common sense and don't go crazy.

Also let your primer cure at least 24hrs.

As for order of assembly / paint. Wow - huge topic and really depends on what you're building and your build style. My only advice is to try and think or look ahead several steps to anticipate areas where you a:wouldn't be able to paint once it's assembled and B: logical sub assemblies that would benefit from being painted prior to assembly. Think car engine...cockpit...tank interior or backside of roadwheels etc...

Most of all just go for it. Plan to butcher a few kits and you'll learn alot as you go.