That is a very good looking bike.
Last night I sat here for ages and wrote all sorts of stuff you might do. But then I just killed it and went away.
I wish you were close by. I'd paint it with you and we could trade tips as it went along. However I don't want to get in the way of what it is you want to do or how you want to do it. I have a pretty set way I do any paint job, it doesn't vary much no matter how complicated the actual end result might be. If something goes wrong, and it happens, I will fall back in the process, but only as far as I have to go and then I'll get right back in step. Basically my process - which is just like almost any other painters - is this. Bodywork if needed->Bare Metal-> Sealer->Filler->Sealer->2K and block->Sealer->paint->clear coat->cut and buff.
Each step has its own sanding regimen except Sealers are never intentionally sanded and as a general rule neither are base-coats.
The single step "Paint" can obviously be quite complicated, but the choices are basically this, either a solid color base-coat, which may mimic a more elaborate method. An example would be House of Kolor's "Shimrin" line. These are colors you shoot as if they were any other solid color base coat but when properly applied they finish like either candy, pearl, or even very fine flake jobs, but of course they are much much easier to apply.
The alternative is to do as I believe you are doing now, which is mix and match your own. That is an ambitious thing to do on a first paint job, and even on a tenth, but the processes work about like this. If you are shooting either a Candy or a Pearl the first thing you have to do is prep to a finer grade of sanding. This is also true of very fine metallic paints, and almost all silvers. Instead of doing your prep sanding up to 600p you will need to go up to 800p or so. The reason is that the pigments in those paints (or the dyes in true candy colors) will line up in the scratch marks at 600p and not look good. This presents a bit of a dilemma in that most paint manufacturers will tell you not to sand that fine, that the base surface needs more "tooth" to assist in the bond. Be that as it may, if its candy or pearl you must sand finer.
The first thing you need with a candy or pearl or even a flake, is a base color. Particularly with candies and pearls the base color will greatly effect the end color, but even flakes when applied at less than full coverage need a background color other than gray, white, or black primer. Generally for candy colors you will use either a silver or gold for the base, something reflective. For pearls you can use white primer and tint it to control your final color or you can shoot any color of base-coat you want and apply the pearl over it. Tinting is the easiest, and least expensive way to go though. Toners, which are very concentrated pigments or dyes, are used for the purpose. Most paint manufacturer's make them, I use Hose of Kolor stuff myself and their line is called the Kandy Koncentrates. A little bottle of it goes a very very long way and only cost a few dollars. It is not only used to color primers or to tint white base-coat though. You also use it to make your own candy colors by simply mixing it with either inter-coat clear or a catalyzed clear. Same thing for pearls, you can add it to pearls, and same thing for flake (dry flake), in that you can mix it along with the flake in your inter-coat clear. Flakes are normally mixed with a clear, either inter-coat- or catalyzed, and shot on. You need a gun with a big cap for this but most "primer" guns have a 1.8mm or larger cap, so you can use them and your carrier has to dry or set up slow enough that the flake has time to lay down. You gain time with your reducer and if you have to paint at night or wait until cooler days. One way or another you have to give it time. The other thing with flake is to decide just how dense you want it. Sometimes you only put enough flake in the clear to sprinkle highlights around. So with those you paint a color, and then shoot over it with a clear with flake mixed in. Most jobs want more though, so you mix more flake in the clear (up to the max recommended by the maker of the carrier) and if you need it denser you shoot more coats. In either case the more flake you put on the less you see the under-color, but its not necessary or even desirable most of the time to completely cover it. You can almost always get better effects by letting a bit of it shine through. In either event though to get the final color you are either going to have to shoot candy over it or, and this is the better way, just mix a toner in with the flake and get the color at the same time. You have to shoot some test panels to find the right concentration of toner (always less than 20% by volume) for the color you want, but once you've to it the color becomes very easy to duplicate from one part to another. Just count coats.
Back to the story. Flake will shoot lumpy, like bad orange peel. So you are going to have to shoot some clear over it and sand it out. As I said earlier I shoot the same clear over it that I will use to clear coat the work when it is finished. Most inter-coat clears weren't made to be sanded. Anyway, once the flake is on and the clear is shot over it the work has to be given time to dry (and off-gas). Two days or more is good. Then block sand it back flat but depending on what you plan to put on top of it (other artwork, or color, or clear) you decide how fine you want to sand it. Clean it back up and tape whatever needs it. Tape will just love it and with the plastic tapes you can do some really intricate things. Also, don't be a bit bashful about taking your ideas to a local Sign making shop - most will be happy to make up vinyl masking templates for you real cheap, which is great if you want to do any logos or lettering, or even intricate designs.
Now the other part. All of that is using two stage paints and process. There is a base coat and then there is a clear coat. We play tricks with the base coat part, but its really all the same. With this method the base coat is non catalyzed paint and the clear coat is catalyzed. You put hardener in the clear coat, none is necessary (though some guys put it in anyway) in the base coat. Well, its isn't all like that. With some paint systems its all catalyzed from start to finish. This is much more complicated and durable way to do a paint job, it also results in the most spectacular finishes, and it is also by far the most expensive and it is the very least forgiving of mistakes. One of the major advantages of fully catalyzed systems is that there is essentially no limitation on film build. Now that isn't true of course, you can't plaster on the paint a half inch thick, but with some custom jobs there can be a surprising number of coats of paint involved; over 20 is not uncommon. With a base-coat/Clear-coat system you want to get it on there with as few coats as possible.
So that should give you an idea of how the world spins and I hope it gives you something to work with to figure out where you are now and where you want to go next. If you've got it sanded flat back to a sound base then your best bet is to just reseal it and go on. I'd get a solid base color on it and then put on the flake. You didn't say what carrier you are using for your flake, but I assume its the inter-coat clear by whoever's paint you are using. When you get as much flake on it as you want go immediately to clear coat. Stay within your time windows. Shoot on 3 coats and let it set for a couple of days. Come back and sand it flat and then add your artwork, the black knee-dents, any pin-striping you want to do, that sort of stuff, then clear coat it with another 3 coats. If you want to go hog wild nuts you can come back a week later and flow-coat it if you like, but that would be like putting sugar on Frosted Flakes, like putting butter on a McDonald's hamburger.
Now, if we were standing around in my shed (paint booth) having this conversation right about now I'd look at you and say "So, what you want to do?"
