to the OP: any particular genre you are playing on the PS3 that you are having problems with?
personally for me, I think kb/m will always better for accuracy, especially for FPS games. I've been a PC gamer for a relatively long time, and only recently started playing FPS on consoles when COD4 came out.
so is that the problem you are having? trying to play FPS? because I can't imagine you having problems trying to play a platformer or rpg.
it does take some time to get use to it, but I can tell you that the PS3 controllers are excellent controllers, light, durable and hold the charge for a long time. the comfort is all relative of course, and you'll adjust your holding and button configurations to suit your hands. My hands are inbetween a L and XL, so I always thought the PS3 controllers were on the small side, and I was wishing for a bigger controller or a xbox 360 controller. Well, when I got the 360, the 360 controller wasn't that much better. for me, the PS3 controller seems to put my hand in a weird position, but I'm very accurate and can play for a long time. The 360 controller is more comfortable initially, but my middle, ring and pinky fingers hurt after a few hours due to the shape of the wings.
But the whole discussion isn't which controller is better, but how long it takes to get use to right? I say if you stop gaming on the PC, and only play the PS3 for a month, you should be fine. Especially play a FPS. You'll hate it for the first few days, but you'll get use to it. If you play multiplayer, you'll come in the bottom half, don't worry about it, just keep playing. If you played everyday, I think by the 2nd or 3rd week, bump up the sensitivity, and keep bumping it up until you don't have really good control, then bump it down so you have good control again. By the 3rd to 4th week, your muscle memory and intuition will take over and I think you'll hold your own. You'll develop your own way of how to aim, and how to move the reticule over to your target, either by slowly moving the stick over a few degrees or by scooting over little by little, and then a combination of the two. On average it takes 21 days for something to become a habit, so I say a month to your question.
I now game about 80% of consoles and 20% on PC. My PC is decent with a 4870 and 3.8 ghz, so it's not like I don't game on it because it can't handle it. It's just more comfortable for me and being in a relaxed and reclined position to play, instead of sitting on my computer chair with both arms on the desk with kb in one hand and mouse in the other. I have L4D on PC, but will use the gamepad when playing co-op and usually come 1st or 2nd in the stats, but will switch to kb/m when I play versus. So it's all about comfort and enjoyment.