The search engine is your friend here, use terms like master cylinder, caliper(s), R1, FJR1300, 4 or four piston, 6 or six piston, brakes, etc. Also try 'vintage brakes' which has a chart listing # & size/pistons on the y axis of a chart and master cyl. bore on the x axis. This gives a ratio # which is then compared to a known value for a 'good feeling' function of the master cyl at the lever.
http://www.vintagebrake.com/mastercylinder.htm
Here is the thread it came from:
http://www.vmaxforum.net/showthread.php?t=17036&highlight=vintage+brakes
This chart may also have had an earlier appearance on the forum. Whatever you do, be sure to count the total # of all pistons in
both calipers, assuming you are doing this for the front brakes.
The early FZR 750/1000 brakes are the same, I believe, and I think 1995 is the only year the FZR1000 used the 6 piston Tokico's and after that I think the bike was the YZF 1000, which eventually became the R1. With the 1993+ VMax 298 mm rotors, any of these calipers will provide better braking. You don't have to spend a huge amount of $ to get them, if you are patient you can find them in good shape at a reasonable price. Of course you can find crash-damaged calipers from these same bikes being hawked on ebay motors for $160 apiece, stay-away! There is a big-enough supply of them available that you should be able to buy both for less than that, requiring nothing more than a good inspection/cleaninbg and some new "HH" rated pads. Sometimes you can even find the front master cyl, lines, and two calipers for less than what the pirates are trying to extort for a single 6 piston caliper.
I think Sumitomo was also a Yamaha brake supplier during these model years, and I am unaware of any preference of one manufacturer over the other.