I was going to ask where did you find how to do this? And is this a job that I would be better sending to the dealership and not putting my noob hands in the mix?
Most dealerships won't go to the trouble of getting the TB's that close (they'll get it with the spec's, 10mm) much less checking it again at 4,000 RPM's as its not in the shop manual.
With all you did, you can easily sync the TB's yourself and it would definitly be cheaper to buy the tool (about $100.00 vs paying a dealership $125.00+.
The unit I purchased and use is a Morgan Carbtune (
www.carbtune.com ). No liquids, high quaility,very easy to hook up and fine tune adjust.. I've synced many of my customers bikes, it's payed for itself many times over and the customer gets to see what it was previously and what it is now(the shop won't let you see what they do). The FZ has a block, (see below picture) just below the three large rubber hoses. Once the Carbtune is hooked up to the four vacuum lines, two on the outside edge of the engine adjacent to the frame, crank up the bike. #1 cylinder(left most cylinder is the base) adjust at the block the other 3 cylinders.. Should you need the shop manual, PM me, it shows which screw goes to which cylinder.
As for checking at 4K RPM's, when I got the bike, it had a typical inline 4 buzz at about 4K that was extremly annoying. I just about sold the bike it was that annoying. Bought the tool, checkd the sync, it was out a little and adjusted. Helped some but still had the 4 k buzz... Lifted the tank again for S &G's, hooked up the carbtune and checked the sync at 4,000 RPM's. The #4 cylinder was not pulling as hard as the rest (the cyllinder on the tool was much higher than the rest) and adjusted it down. At idle, it was still well within spec. Just kept fine tuning it getting it as close as possible at idle and 4k. Got rid of approx 80% of my 4k buzz...
When syncing, especially fine tuning, I strongly recommend putting the largest fan you can find at the front of the engine as the engine needs to be to temp.
*As noted above, the block where you do the adjustment adjusts sync at the lower RPM's (up to approx 4k, once the throttles open further than that, doesn't make much if any difference). On the FZ, like my 150 HP, Yamaha 4 stroke, FI, outboard engine, the engine uses
TWO throttle bodies
Two butterflys in each. You can see the adjusting screw inbetween the TB's in the picture. Its set from the factory and SHOULD NOT BE TOUCHED... Somewhat related-when I paid a Yamaha dealer to sync my FJR, they adjusted one of those screws (again a NO NO). (and I'm paying them to screw up my bike!). I know this as when I checked under the tank, Yamaha, at the factory, puts a small dab of white paint on the adjuster screw/spring. Mine was turned approx 1/4 turn. The FJR is considerably more difficult than the FZ to get to the adjuster air screws. Once I had the Carbtune, I put the screw back to stock and re-adjusted the sync per the manual.
The K&N oil filter isn't re-usable. The K&
P, which I use is:
Custom Oil Filters - Reusable Oil Filters - Cleanable Oil Filters - Green Oil Filters
As for changing the oil again, if it was that dirty, IMHO, I'd change it again (with a filter) if you plan on keeping the bike.
I have my idle set at 1,000 RPM's hot (below the recommended 1,300) so you may want to raise it. The charging system is NOT charging at 1,000 (at least with the dual headlight mod) and is running off the battery. At 1300, 1350, mine is charging just above the battery, about 13 volts...
Pay attention to the engine on the first hard run, I hope you didn't strip out the aluminum spark plug hole.... You'll know it if the plug blows out of the head..
(Picture below compliments from another member's post)
:thumbup:
. I forgot to put dielectric grease on plug 1 and 2 but I felt the cap and plugs secure (clicked down) and 3 and 4 were a lot easier with the dielectric grease. Also I checked the plug caps that the wire was snug and unable to rotate (2 of them (2 &3) seemed to tighten up a little). 
