Cost Effective way, cut the hole in the floor to the correct size. It will allow proper air flow also. Otherwise, you can order registers online from various sources. Normally come in white or brown, otherwise there are specialty ones also.

http://www.floorregisterresources.com/products.php?cat=7

http://www.floorregisters-n-vents.com/White-Steel-Louvered-Floor-Register.html

You might consider replacing the "boots" to a common size, then just purchasing standard size boots. You may come out cheaper in the long run and get a better selection of grilles. As long as the boots are accessible, you can easily change them. If you have wall grilles, it may be even easier since a "wall stack" is usually used. That's just a duct the size of the wall space. Take a grille off and see what's behind it. It may be easier than you think. Duct boots are usually just attached using a couple of roofing nails. Just stick a screwdriver behind it and pry a little. You can purchase the standard size boots at your local home center or just hire it done. Either way it might be cheaper. I've had to have custom grilles made and it's usually pretty expensive. Also, you might want to consider sealing your ducts while you're in there. . It will pay back several times during first year. Here's an article I wrote covering just this topic Duct sealing.

Another option may be a company live Vent Covers unlimited. There are several others if this is the road you want to go down. Can you post the measurements that you current have for the vent covers?

Hi! If you are living in or around bay area, we provide wide variety of services for Ducts ( Installation , Cleaning , Replacement, Ductwork Repair, Duct Sealing, Upgrade) Please contact us for any help. Our rates are very affordable !

Thanks,

Mani

BayAreaDuctServices