Can you? and Should you? are totally different questions..
Can you....sure- but once you get the rest done (your injectors cleaned, your new fuel/ignition mapping and a different exhaust installed) your synchronization will be different
but considering you purchased the tool, and by the sounds of may ride it prior to getting everything done..... You should go ahead and get them synchronized now and then when you get all done with everything do it again
I think the service manual states to do it every 7500 miles anyways (many bikes have that interval or less for synchronizing)........ but in my practical experience most of the bikes I have seen numerous times, after I got them "perfect" once it was rare to have to move them much ever again, often less than 1/16th turn on one screw, sans having something significant done to the bike to change this
That said, the first time seeing numerous bikes (like I bet 90% of the bikes I see) the throttle body/carburetor sync is off by 2 even 3mb which is huge..
I have just for shits and giggles checked throttle body sync on several of the C14's I have seen numerous times;
ie...
bike comes in first time ever, check the sync before doing all the work but don't change it- just note the values..... then do the entire Tune up procedure and make the necessary changes to get them dialed in perfectly....
then the bike comes back again 15-20,000 miles later for another tune up and check to see how much the synchronization has changed before doing the rest of the tune up, note where it is at (often 1-2mb off) and then do the tune up and check again (rare to have to make adjustments now)
But I see about a dozen or two bikes every year I end up having to pull the sync screws out - fi bikes - (along with the spring, the washer and the o-ring) so that I can clean the tip of the adjuster screw and the passageway the air goes through
And cleaning your injectors is a very good idea for the smoothest running and best power output........