Ill add my two cents on this one. Ive been meaning to make a write up but havent had much internet access lately. So here's a quick rundown on my setup. Sorry if this is redundant with what others have said in this thread, I only skimmed it over.
Im running a 2003 R1 front end. It was a very simple swap thanks to one custom made piece. Modking(=badass!) made me a custom one off lower tiple to mate the R1 tubes to the FZR stem. This made my swap a direct bolt in. I originally intended to just use the stock R1 lower triple, but after welding up a stock stem to make the size difference up it warped slightly. It was only a few thousanths, but I didnt trust it. So I sourced another stem and went this route. Mine was the protoype and last I heard the design was modified a bit, but the effect is the same. I sent him my stock R1 lower triple and he was able to take the dimensions off of it and make a new one out of a big honking hunk o' aluminum.
R1 triple trees
Different generations of R1s had different front end geometrys. 99-01 triple trees will not mix with 02-03 or 05+. The tubes will interchange, but the spread between the tubes and the relative location to the stem is different. So an upper triple from a 2000 will not mate with a lower triple from a 2003 model. The tubes are all 50mm USDs and will interchange, but if you're piecing your front end together like I did, make sure youre upper and lower triples are from the same generation R1. I am not certain on this, since I have not messed with the later years, but I think the 02-03 triples are the same measurements as 04-06, but dont quote me on that.
Another necessary modification is a simple bushing for the upper triple. Since the FZR stem is a smaller dia. than the R1, it is necessary to take up the difference. I was lucky enough to have acess to a metal lathe and made my own in about 15 minutes. I made it with a press fit into the upper triple and a snug slip fit for the stem. It also has a lip to butt against the triple to keep it from working back out.
Also, the FZR stem is smaller than the R1, so to make the difference, many people will weld all the way around the mating surface at the bottom and then turn it down in a lathe to the proper press fit diameter of the R1. This is risky since the heat can warp the stem, and did with mine. Many people have used a bushing with good success, even in racing applications. The difference is very small, so its usually necessary to bore out the lower tiple a bit. Then a press fit bushing is made with the ID=OD of steering stem. Bearing OD=lower triple ID. When modifying the stem be sure to accomodate for the ring at the bottom. This will keep the stem from walking out of the triple once its pressed in.
Wheels
Many sources say that the 99-01 and 02-03 front rims will not interchange. I have one of each and they are pretty much the same dimensions. The axle dia. is the same, the wheel bearings are the same part number, and the rotors are the same size. The only difference I can tell is the spread between rotors. This can be rectified by using a washer to space the calipers out slightly, but if at all possible I would recommend getting a matching wheel to the year and model you are using.
Tires
The R1 front end is slightly shorter than my FZR front end was so instead of using a 120/60 front tire, Im using a 120/70 and it brings everything a bit closer to the stock height. I wish I knew more about how the geometry affected handling, but unfortunately I dont yet. Working on it though
Brakes
Different R1 years have different brakes. Outwardly the differences are not really noticeable and the brakes will interchange between 99-03 as well as R6s and YZFs. The change to radial calipers came in 04 to the R1s. These will only work on the same generation forks. Im actually running R6 calipers, but the difference is negligble. The biggest caliper improvement to this type caliper came from the 02-03 R1. These calipers have gold pots intead of blue. These calipers are slightly lighter, but thats about it. If youre not getting a complete front end youll need to source a master cylinder as well. They all interchange though from YZF, R6, and R1.
Fenders
The FZR fender is ugly. R1 is pretty

. I wanted one in shift red to match my R1 tail, but that color was not available until 04. I found that 04-06 fenders will bolt right up to a 02-03 front end with no modification necessary and I managed to find a brand new one on ebay for about $35 shipped.
Clip-ons
FZR clip-ons will not work since the fork tubes are different sizes, you will need either stock R1 ones or aftermarket ones for that model. I used aftermarket ones and added R6 controls on the left side, used the stock FZR throttle tube and controls on the right side.
Ignition
the stock ignition cylinder will need to be modified slightly to fit the triple. I used some small aluminum tubing to make up the difference. Some scrap metal and a little inginuity took care of that pretty quickly. Im sure you could take a stock R1 iginition and key and swap the harness plug to make it work. I still have yet to come up with a suitable fix for locking the steering though.
Thats pretty much it. The only fabircation necessary is getting the FZR stem into the R1 triple. The rest is parts sourcing. I had great luck with ebay and from what Ive seen, you can get most or all of the parts to do this for $500 or less. Generally less if you can find a decent undamaged front end. The bushing is super simple and a machine shop would cahrge very little. in fact, Im suprised no one has made a run of these yet and sold them.
