I think the confusion here is the original poster was asking if he could put the OEM headlights from an '03 into an '06 that came with halogens. Everyone is suggesting buying an aftermarket kit and using it with the stock '06 housings.

I don't think aftermarket kits are as good as OEM, but I think they are a lot better then stock halogen. So I'd suggest getting a good retrofit kit too.

 

I put Hids in my 05 zx6r and i have two different sets of bulbs for the kit. Rebased h7's with the correct focal point and d2r bulbs of a slightly higher K. The rebased bulbs have a sharper cutoff and more precise beam pattern than the general d2rs, but the difference is only noticeable if you know what your looking for. All my friends say that its crazy that I have hids on the bike because they can literally spot from over a mile away in a sea of traffic but none of them come running up to me saying,"hey, your lights dont look factory or dont project the proper beam pattern."
I understand totally what the original poster is talking about and honestly, I dont think its worth the hassle to do a full scale retrofit unless you dont care how much its gonna cost because it aint worth it IMHO. If it matters, my kit has Denso ballast/ignitor with phillips bulbs.