The starting point for creating your own water slide decals is to obtain the correct clear backing. It is easiest to start with a ready manufactured sheet of clear decal film. There are several sources; most online model suppliers carry this material. Some suppliers even claim that their paper is manufactured especially for ink jet printers. Secondly there are four methods I am familiar with:
Creating masks for each color separation, masking the clear decal film for each color and applying the colors from lightest to darkest. Or hand painting the design if you're really good at it. Good points: Not too difficult and inexpensive. Drawbacks: Tedious and time consuming if you have to make multiples. Masks have to be thought out and made well.
Silkscreen process. This is a process many of us learned in school. I will not go into detail as any good art book can describe the process far better than I. Pro: Good quality and not too difficult a process if multiples are needed. Con: Alignment can be tricky and skill is required to set-up.
Produce the desired image on a computer, or by hand, or from a photo of the prototype and then take it to a print shop and have it copied on a color photocopier to the clear decal sheet. Pro: Probably the cheapest and easiest set-up for most people. Con: The quality of the final product can be compromised by the quality of the copier and dyes.
Produce the artwork on a computer and generate it to a printer. You can use any common program like Corel Draw or Adobe to do this. Pro: Not too hard for a novice to create, or scan the artwork and many people already have the setup without knowing it. Con: If using an inkjet printer the ink does not always adhere to the paper well and must not be handled until dry. This method works well with Alps printers that use a wax ribbon, but Alps are expensive and I believe they no longer produce printers. A friend used this method to make his own decals for a NASCAR "Superman" logo and the result was very good.
There is also the possibility of having a decal manufacturer produce the decal you want, but that is very pricey and it won't happen overnight. No matter what method is used, you will need to spray a clear coating over the decal to seal in the inks, dyes, etc., as they will run otherwise.
You do not have to prime before painting, but I prefer to for several reasons. The first being that a primer will show any flaws in construction and I really like to find those prior to the final paint scheme. A primer will also help to show if there are any areas where might not stick sufficiently.
The primer coat can also be useful if you wish to paint a lighter color over a dark plastic, or even to get a more uniform coat. Most importantly a primer should help with paint adhesion, but a primer is not a must. I have gotten into the habit of washing a model in warm soapy water before painting. It is very important to make sure all traces of soap are thoroughly rinsed off.
I would not prime anything prior to assembly, as that will negatively affect the adhesion of the glue. As I mostly use an airbrush I usually just spray everything once assembled, though sometimes I just spray areas that I have put a lot of work into. Some small parts like you mentioned do not really require any primer and if hand brushing would just make for more work.
Now then, A #10 xacto blade is the best way to open doors and trunk, you will loose some material but not much as long as you take your time and make small cuts. The kick panel can be replaced with sheet styrene covered with bare-metal foil, I swear by that stuff. Actually, best hinge material for me has been paper clips, easy to bend and work well.