Wiring is somewhat simple, the CDI and the alternator are the main two things that change, everything else is based off those mainly.
Since this is a go-go type of machine, are you planning to run lights? No lights makes the wiring quite a lot simpler. When I make "race" harnesses with no lighting, they tend to run about 1/2 the cost of the full OEM style harness.
Alternator designs are mainly single phase (1 wire + internal ground like the 200x engine, or 2 dedicated wires like the 200s,200m, 185s, etc use), and the larger older machines, or the newer machines generally run 3 phase which has 3 wires from the stator. The physical way the power is generated is slightly different, but the only thing that really cares about that is the voltage regulator/rectifier if the machine even runs one. Like the 200x, there is no regulator, the lights use 100% of the power from the alternator which is about 70w. You can convert to LED to get more light, or buy a high output stator that has more windings than factory. Either case, if your lights draw less than max output, you'll have to atleast have a voltage regulator (2 wire like the 350x, 250r, etc), or a single phase voltage regulator/rectifier (generally 4 wire, 2 for AC in, and 2 for DC out, the AC and DC can't share the same ground so the 200x would require the battery and everything DC to never be frame grounded (floated ground)).
I'm not familiar with the turbo setups with carbs, but isn't the tank still physically above the carb, and with equal pressure on both sides of the fluid, shouldn't it natrually go down to the carb via gravity? You mention up to the carb, but I doubt you're mounting the tank below the engine. For the alternator, as the name suggests, it creates alternating current, aka AC. Very few machines generate actual DC power, it's effectively an electric motor that is being spun to create a charge normally called a generator on old car engines. Anyway, 100% you'll need a rectifier in the system if you plan to use 12v stuff which also means you should have a battery too. The simplest way is probably the single phase regulator/rectifier route and float the DC side of things, which means the fuel pump can't ground through the housing, it needs 2 dedicated wires. I have a couple regulator/rectifiers I've found, but haven't had a chance to test (I don't like bare hands in the cold and I'm in Michigan lol). One is an OE branded voltage regulator (no rectifier for AC to rectified DC), and the other is aftermarket designed for motorcycles. Both rate 200w+ so on paper they should work fine.
Again, I don't know the ignition timing requirements for turbos, but the stock CDI has a conservative but solid timing curve designed exactly for that engine. You can adjust the pulse generator (pickup coil in the automotive world) to advance the ignition timing as a whole to push the limits a little more or pull back the timing. Personally I'd stick with stock unless you really need to push the limits and know what you're doing. The basic concept of a CDI is basically it gets it's power from somewhere which on the 200x is the exciter coil (another coil on the stator that's high voltage), it has wiring for the pickup coil to know when to spark, also of course the output to the ignition coil to create the spark, and a kill wire to stop ignition. The timing in them is based 100% off the rpm of the engine. I haven't used a programmable CDI yet, but I suspect you'll get x number of points you can program, so like less than 500 rpm you have super retarded timing for easier starts, 500-1200 for your idle timing, etc till the max advancement at max rpm. Some likely have a rev limiter that can be enabled, I don't think the stock one does.
For a battery, you don't need much, it's basically just a voltage stabilizer. In theory a large capacitor would be possible too, but that gets a bit more advanced. For which battery to get, I'd stick with Honda stock brand Yuasa. For the size, it depends on the space you have, but here's the stock size for an atc200es - YB14A
https://www.yuasabatteries.com/battery/yb14a-a2/
If you're building the harness yourself, I'd 100% suggest getting the "B" crimp style crimpers and OE style terminals that are quality, not the cheapest ones around that are made in china on Ebay. When I first started out, my main source for tools, terminals, etc was here.
http://cycleterminal.com/
The individual connectors and such add up pretty fast. Good news is, you won't need any battery cables since you don't have electric start (or are you planning to get the Goki starter for it?). The 6mm ring terminal fits the battery well.
On the whole knock thing, are you talking about predestination (pinging), or a knock like a rod knock? Besides the extra heat and more power, I don't see how the turbo is any different from a well built engine. You'll need high enough octane fuel to handle the compression + extra air from the turbo plus the heat etc. You might need to upgrade the rod if anything is made, I don't really know the weak points of the 200x engine. Generally speaking, turbos respond well to lower compression (more air/fuel can be crammed in the same area), atleast that's what the diesel guys do. You can put an ATC200S piston in the 200x to lower compression from 9.6:1 down to 7.8:1. If I remember right, low compression also offsets some of the extra heat from running the turbo. Again, not really my specialty, just observations.
200s specs - https://atvmanual.com/honda/atc200s/1986-specs
200x specs (you didn't say year, but assuming 83-85, the most common years. If it's 86-87, then it's a completely different designed engine) - https://atvmanual.com/honda/atc200x/1985-specs
If you don't know the year of the engine, you can type the engine serial number in my vin/serial number decoder. Pretty sure it's lower left side of the engine below the sprocket.
https://atvmanual.com/honda/interact...er-atv-and-atc
Hopefully I didn't go too crazy with the electrical talk, if something doesn't make sense, let me know and I'll try to clear it up.
My site is somewhat new (about a year old), but I do plan to add the alternator types to the spec pages and maybe a quick reference table. My data source that has been quite accurate is the wire diagram in the Honda service manuals. They show good details like if it's internally grounded and such. I'm always open to ideas, I'm currently in a redesign of the back end of the site to make it more flexible. I built everything from scratch, no privacy stealing code and such except what google does with google analytics/adsense and such. Also very little java script, so the pages load fast and process fast.
One thing you'll need is a wire source. There's a few guys on ebay that sells wire that's not bad quality. I personally use wire rated for fuel injector harnesses (high temp) which makes it a bit stiffer than the other stuff, but the insulation doesn't melt so very friendly for soldering and such. I should have all colors you'd need on hand if you wanted me to put together some type of kit, just not sure how long you'd need for each color. Green (ground) will likely be the longest you'd need since it goes to nearly every part. Another route you could do is use the stock harness if it's long enough and add the extra wiring to the harness. That would solve the CDI/engine wiring, you'd just have to tap into the lighting coil wire and run that to the regulator/rectifier and add that stuff all external to the main harness.
Anyway, good luck with the project, welcome to the site, and we always love photos =).