I am converting from a c10 86 electrical system to a post c10 94 electrical system. What problems and modifications do I have to contend with?
I'm going to ask a question, please bear with me; "why" are you wanting to change this out for the post '94 system?
Does your bike start, and run, correctly right now? Have you ridden it for any specific long distances, without issue? how many Miles?
Is your existing system not working?
If not, have you gone thru it all, and found issues? And what specifically were they?
Switching over is not simple; It ends up being very costly,(i.e. time, and money)
and a lot of work, so on a bike that is worth less than $1500, the added benefits (if any), will not make it worth while. Also, even if you have a "new" harness, "new style Gages" do not fit the fairing, or mounts.. just commenting. There is nothing about the "newer / gen II " wiring, that sets it above the Gen I wiring system, and even places it lower, as you loose the "backup emergency headlight system".. the '86 came with.
I only comment on this, because of the level of time you will need, and the lack of people here that have great patience to "walk ya thru it", which I have done quite a few times over 17 years here, may leave you pounding your head against a wall, and asking "what was I thinking"... frankly I hate to see people struggle, and spend money, without having a bike to ride.... for months.
so, to address part 2 of your question, as to parts..
Harness, all, front to back, replacement
Left hand control switch pod, differs in pinouts, from both
emergency headlight system loss
J-box internal differences, even tho they all plug and play(somewhat, but at a loss of ampacity on some circuits)
Gauge cluster, and subsequent mounting
Fairing (front internal and external, and sub frame)
and mainly, emergency service and repairs to a bike's system, when on the road, where there is no explanation to anyone attempting to help repair (service technicians), as to all that has been changed out, or what is Original or Not. (i.e. replacement parts, in emergency repair)
There are a LOT of pre '94 bikes running perfectly today, the system is what it is, and works fine.. likely your fuel tank will rust and leak, before this electrical system goes titzup. If it's running, just ride, if it isn't running, ask for guidance in repair, but please don't rip everything out, prior to an easy repair.
oh, crap, I just realized this response I made, was to a "one post and poof/gone" o/p, back from December.. with no return.. what a waste of time.