I wish you had posted your plans for this before you posted your results from having done this. The very first thing I want to ask you is why you used boat paint on a motorcycle and the second is what did you use for primer under it?
On that Harbor Freight gun you are using, is it the purple one? If so it might surprise you to find out that its actually not too bad a gun despite its amazingly inexpensive price. You didn't say anything about how you have the gun set up and you didn't say anything about how your reduced your paint (its called Reducer, not Thinner) or with what. So there's nothing that can be said to help you with your runs other than tell you how to set up a gun and reduce the paint when the proper materials are used.
OK, let's start with the gun. First off somewhere on the gun's handle it probably tells you what inlet pressure is required to get 10 pounds pressure at the cap, if its not stamped in the gun get it from the manual or manufacturer's website. This number is important but not necessarily the pressure you will use. Get yourself a small regulator/pressure gage and put it at the gun's handle then with the trigger pulled back to allow air flow set the inlet pressure at the gun to what the manufacturer recommends.
Next, there will be two or three controls on the gun. There may or may not be a control to let you adjust air pressure at the cap. If your gun has this control it will either be at the bottom of the handle (Iwata style) or it will be on the side of the gun (Sata style). Hold the gun's trigger back to allow air flow and adjust this knob tigher until the handle pressure increases, then back it out until the inlet air pressure stabilizes, and then readjust your inlet pressure to manufacturer's recommendation (probably around 20 pounds (1.3 atm)). Your next two controls are fluid feed and fan control. We'll start with the fluid needle.
The fluid needle really just controls how far back you can pull the trigger. So first screw the adjustment needle all the way in (DO NOT overtighten it) and then holding your finger on the trigger to pull it back lightly unscrew the adjustment, while counting turns, to see how many turns it requires to take it full out. Then set the fluid adjustment at the half way point. Normally it will take about 4 turns from full in to full out. This is just a starting point but its a safe one, set it here and you will probably not get runs, but you will also find yourself turning it out farther with time. Many experienced painters (but not me) will run the wide open.
Finally you have a knob that adjusts your fan pattern. For this one tape a length of masking paper to the wall and shoot a test blip. By that I mean hold the gun about 8" back from the wall and very quickly blip the trigger open and close to shoot out a squirt of paint. The pattern that sprays should be sort of cigar shaped but of about consistent width from top to bottom. You should also have good atomization of the paint. Here, by adjusting that last knob you should be able to get a good even coverage and fan width (set it to match the manufacturer's recommended width) suitable to the gun. For most full sized guns that width will be about a foot, for touch up guns six to nine inches. If you don't have good pattern or spray make minor adjustments to your inlet air pressure.
Next comes your paint. Stick with a system. By that I mean by the right paint for the job and then use the reducers and other amendments that the manufacturer suggests. Do not mix one manufacturer's paint with another's reducer. Once again, stick with a system. As for automotive reducers; they come in different speeds to match your painting temperatures. Also, virtually all automotive paint manufacturers have technical data sheets that will tell you exactly how to prep for the paint, how to mix it, what size gun to use, what the drying and recoat windows are, everything. Read that sheet before you shoot.
And finally; if you want a really good paint job get advice from some real professionals. While this is a great site for all things Honda-Four its not very good for refinishing information. If I may suggest a web site where you will get immediate attention and no nonsense answers from extremely knowledgable professionals try this site:
http://www.autobody101.com/forums/ For others, the very best thing you can do with a freshly sandblasted frame is to immediately clean it and shoot it with two coats of a good quality epoxy primer. Even if you had to thin it down with acetone and paint it on with a brush it would be better than not doing it and far far better than using any rattle-can primer. By the way, that purple Harbor Freight gun is often recommended as a primer gun with a 1.7mm or so cap, but the best primer gun made (Iwata Gunza) only cost about a hundred bucks.
