The only problem you could run into is whether the paint is chemically compatible with epoxy. Generally speaking, 2-component finishes are compatible with other 2-component paints. 2-component means the material uses a catalyst/crosslinker/hardener. There are limits to this however - polyester resin is 2-component, but will not adhere to epoxy and vice versa. I know for a fact that commercial 2-component waterborne polyurethane will stick to epoxy as does oil based polyurethane.. but epoxy won't stick to polyurethane. Some automotive paints are urethane based and others are lacquer based. I think it fair to say that a urethane paint will be a "slam dunk" whereas lacquer may not. You would need to do some test spots to determine adhesion before painting the whole thing. At minimum, use scotchbrite to break the sheen of the epoxy to aid adhesion. Better yet, use some 220-320 grit abrasive (sandpaper) to break the sheen. A quality finish/paint should adhere provided the substrate is adequately abraded. I may be making a mountain from a mole hill, but I'd hate for someone to have their paint peel.
As for the rudders - I haven't found a huge benefit from the height of the rudders as much as depth. Meaning a rudder that is wider (protrudes farther off the back of the boat) will provide more positive control than a narrower but taller rudder. If you read my thread about my SI3 flat bottom boat, you will see the "evolution" of my rudders on that boat starting with the rudders the plans outlined and the two revisions I made to improve steering control and response. Post #43
http://www.rcuniverse.com/forum/rc-a...-bottom-2.html
You don't expressly need to have your rudders' height match the height of the propwash. 1/2-2/3 of the propwash is totally good provided the width of the rudder is adequate. Do test your initial rudders first though - if it doesn't respond quickly or turn sharply, you will need to adjust the throw and/or the size of the rudders.
Besides building a strong hull, your rudders need to perform A-1 perfect. It's a real PITA if your boat don't turn for crap and she gets stuck in the weeds requiring going for a swim or canoe ride to recover it. I learned the hard way a time or two.