I’ve had a Namco for a long time now, and I’ve asked this question many times in this forum.
If you did mod it, the Sanwa would be tall, and you have to cut up the sanwa, it’s not worth it. Also, 99% of the time to mod it you would be taking out the hori PCB and replacing it with a DS1 PCB, so all in all, you are just gonna use the case, and try to shove all the Sanwa parts in it.
Or you could keep the namco (with buttons more sensitive then sanwas, they might feel cheap, but they are more sensitive) and make box for the Sanwa parts. Makes alot more sense. And the Namco is one amazing stick stock, period.
You CAN, buy different balltops for it, (they fit) which is kinda nifty.
EDIT: and while it is great for 3-D, it’s great for 2-D as well, I don’t play very many 3-D fighters, but I do use it for MvC2/3S/KOF/CvS2 and it’s great.