Yeah, definitely don't use ModelFlex to brush, it's not a terrible paint, but it's finicky and as Josh said is only for airbrushing.
Your problem is probably the paint and the brush, The best paint you can buy is Tamiya acrylics. They have an excellent formula and brush on smooth and even. Plus they are comparatively quite cheap and can be thinned for airbrushing. Also, they have clear colors that work great for taillights and turn signals.
Unfortunately Tamiya doesn't make any railroad specific colors, which won't really matter for your trucks, but, if you need to paint a railroad model, try PollyScale Acrylic Model Railroad colors. They're more expensive than Tamiya, but they work great for brushing and can also be thinned for airbrushing.
As for the brush, don't buy the crappy plastic brushes at your LHS, go to a good art supply store (Michaels will work) and get a few different types and sizes made from real hair, if you're at a decent shop one of the clerks will probably be an artist and can tell you what each brush is designed for.
Those brushes are expensive, but if you take care of them, they'll last for a long time.
Finally make sure the paint is mixed really well, if you're going to be airbrushing sometime in the future, it's better to stir rather than shake so that you don't stir up solid particles off the bottom of the jar, however if you won't be airbrushing you don't really need to worry about that. Whichever way you mix the paint though, do it for awhile, 1-2 minutes at least.
I'm not a big fan of painting either, it's probably my least favorite part of the hobby, but I've found that if I set aside a large block of time, and plan everything out ahead of time, it's really not so bad. Make sure you have some water on hand before you start, and plan out how you will apply the paint and it'll work out well.
Chris