Hi Fudgers--
I recently posted a photo of my painted Flea, now named "little kahuna" (thanks Brother Uke!). Here's what I did, and I can't hear any difference in volume or tone, although admittedly I am no expert:
I bought a used Ukeberry (blue) Flea--I wasn't concerned about color because I knew I would paint it anyway. I haven't seen a Natural Flea in person, but if it is just clearcoated pine then it would be alot easier to just lightly sand prior to painting than to have to sand the color off, which is what I did. In fact, sanding the soundboard near the outer edges becomes quite difficult, and as you can see in my photo I ended up with clearcoated pine in the center and the paint covered the not-perfectly-removed blue around the outer edges.
(Aside: my design required bare wood for the center section-if you don't need to see the wood, arguably just a light sanding of any colored Flea, enough to get the new paint to adhere, would suffice, depending on how many coats you intend to follow up with).
I didn't use any type of paint remover, I was nervous about affecting the thin wood (although maybe someone will chime in if they know about using a chemical remover).
I sanded just enough to remove the paint, trying not to sand the bare wood anymore than necessary.
First, I taped off the sections, and did a light primer coat. Then I painted the green (2 very thin coats--always thin when spraying). Let it dry. (the hardest part is waiting between coats!). I next applied the black auto detailing tape, which is very thin. Then I taped off the area for the red stripe, and gave it 2 thin coats, just enough to cover. Finally, a couple of very thin clearcoat sprays.
I used Krylon Interior-Exterior rattle can paint and Krylon Acrylic ClearCoat-available at WalMart and everywhere (are you in the US?)-they have a good color selection and I've had good results with them on all sorts of things like outdoor furniture.
I've been very happy with the result, and the Flea is so loud to begin with, I haven't noticed any problem sound or tone wise (the red Kala's I put on seem to have big volume too).
Again, I'm sure someone may have a more professional method, but this worked for me, it's a fun conversation piece, I live at the beach so it even fits my home decor--and since I've done it once, I don't worry if it gets chipped I can do it again! (But it seems pretty tough to me).
Good luck--I say go for it and you'll be glad to have your own customized Flea!
Mahalo,
david e
ps in the photo the red edges don't look so fine, but they came out very well in person
Edit: NatalieS's reply came in while I was typing, and I have to say if you are buying new this sounds like a great option. I bought used to save a few $ and so I wouldn't feel so bad in case I screwed up!