What size is the XJR master cyl bore? Our stock size is 5/8 and if you deviate from that for the R1 calipers that could be your problem, as the R1 calipers are similar to the stock dual-opposed piston stockers on the 1993-07 bikes, for the amount of fluid and bore size needed.
You might try a reverse-flush on each next time, that may be quicker. I used to do a Mity Vac on both sides, but for some reason, I found the clutch side went faster w/a reverse-flush. Now I pretty-much just do the reverse flush for both.
Here's a thread about the FJR master cyl, and links to useful charts for calculkations about 'what will work:' http://www.vmaxforum.net/showthread.php?t=17036&highlight=master+cylinder+bore+size
You might try a reverse-flush on each next time, that may be quicker. I used to do a Mity Vac on both sides, but for some reason, I found the clutch side went faster w/a reverse-flush. Now I pretty-much just do the reverse flush for both.
Here's a thread about the FJR master cyl, and links to useful charts for calculkations about 'what will work:' http://www.vmaxforum.net/showthread.php?t=17036&highlight=master+cylinder+bore+size