If you replace the cam chain and after removing all the necessary bits to get to it including the plugs. Check the tappats first as now is a good time to replace any shims, remove both cams but do not remove the sprockets. there is no need.
This allows you to turn the engine over to feed the new split chain through the tunnel and around the crank without destroying your valves.
Line up the exhaust cam first and then roll the inlet one back in, a little bit of trial and error and frustration if you don't get it right first time.
All cam and crank marks should line up perfectly.
The best way to check if the chain is worn is to see if the timing marks line up.  a worn chain can be up to one tooth out in the timing. The timing on my 600 was over one tooth on the exhaust side and the chain was a link and a half longer than the replacement. The tensioner was not at the max but about 5 notches from the end.

I get most of my parts from www.cmsnl.com I found them great to deal with and plenty of communication if there is a delay or out of stock. Click on search by part number and away you go. Good site for checking prices also. They cover Honda Suzuki and Kawasaki also.

Do not fit a used cam chain as it is false economy.  BUY A NEW CAM CHAIN
http://www.wemoto.com/bikes/yamaha/fzs_600_fazer/98-99/picture/cam_timing_chain_tourmax_-_rivet_link/
http://www.wemoto.com/bikes/yamaha/fzs_600_fazer/98-99/picture/cam_timing_chain_tourmax/
Remove the tensioner and check it is moving freely oil it well and highly unlikely you will need to change it.
 

Well worth the investment, but make sure you check the TPS setting after balancing the carbs

I have found over the years that the pluck caps loosen on the leads and can give a bit of hesitancy and sharpness is gone.. Many wrongly assume the caps give trouble and change them when all it needs is the following: Remove the caps from the leads cut a 1/2 inch off the end of the leads and screw them back on again. Water in the carbs can also cause the issue if the bike is used in the rain a lot or stored outside in the rain. Draining the float bowls and changing the fuel filter will solve this. Water lodges in the filter as it is resting on its side and can get picked up by the carbs when it hits the power band arounf 7000 revs
The above can also cause the odd backfire when starting from cold.
Check the TPS setting especially after balancing the carbs.

I get about 50 most of the time to and from work,but  have on a few spirited occasions hit low 40s and wandering through south of France last year with 2 up got 66. On a track day it has never dropped below 40.
Only mods are K&N Filter and Iridium plugs.
 

Out of curosity, will it rev with the choke on?
 

Just recently bought a grab rail for my sons Fazer 400 from the Japanese Site http://japan.webike.net/. Part number is HA6471B. Depending on the exchange rate it may be a little expensive, Cost me €90 inlcuding postage, but it is a well made bit of kit and takes about 20 minutes to fit. Makes moving the bike around easier and adds a bit of security for passengers. Most amazing was that it took only 5 days to arrive from Japan to Ireland. The site itself has an amazing amout of accessories for all bikes.
 

Just came accross this when searching
http://www.ebay.co.uk/itm/Yamaha-FZ-400-4YR1-96-EBC-CK2371-Clutch-Kit-/150696962004?pt=UK_Motorcycle_Parts&hash=item23163d27d4

Hi Dude
 A little bit of confusion here, the oil filter of the carburettor version of the 600 is different but the one for the under seat pipe fuel injected version is the same, which is most likely what you would have been supplied with. The FZS600 98 - 03 is much shorter than the 400 one and this is due to the oil cooler fitted to the 600.between the filter and the engine.
 I had a used set of 400 inlet manifold rubbers and they were not exactly the same size. Maybe because they were knackered they did not measure up but they were close in size. However I have a new set for a friend’s 600 on order and will check them with a damaged set of 400 carburettors  I have in the garage. This will be brilliant for 400 owners because the 400 ones are over double the price of spurious ones for the 600 and I need a set for my sons 400.
Back to the exhaust, yes it does fit straight on to the 400 but it is not the same  Would hate to be a 600 owwer and be sold a 400 one. I had one on my sons for his test; he took it off again after passing. The downpipes will fit, even the exhaust gaskets are the same size and part number.
I'd say together we should be able to help many owners out there.
If anyone has a standard 400 exhaust I am looking for one.
Regards
 
 
 

Check the tappats first, as the service schedule for the tappats is 24000 miles and check the valve timing, all the marks should line up exacly, if not then the cam chain is mostly likely worn and needs to be replaced. It is rare for the tensioner to give trouble on the Fazer. I replaced the cam chain on my 600 at 50,000 miles with a split chain from Wemoto and it now has 65000 and still ok. It was rattling for 5000 miles before I got around to changing it..

 Send me the code under the seat, it will be something like 4yrx 010 x and the frame number, it will be something like 4yr 00XXXXx (patj_duggan@yahoo.co.uk)
Then I can send you the exact parts catalogue. All parts are easy to get from the Yamaha dealers if you have the part number
 
Somebody has already uploaded the silver version catalogue and the converted word version of the owner’s manual I created some time ago. Unfortunately they were all in Japanese but I gave the parts file English names.
 
 I own a 2003 Fazer 600 and my eldest son had a 1997 Fazer 400 (4yr1) and now my youngest son has a 1998 4yr3 model.
 
The 400 is designated the FZ400 in Japan
 
Having both bikes in the garage I was able to compare them and during servicing and repairs I discovered the 400 is almost exactly the same as the 600 with the following main differences.
 
These major differences are:
The Carburettors
The Clocks
The Headlights.
The Lower fork sliders. (Stanchions are the same)
Fork Seals
Fork Seal dust caps
The Exhaust  (downpipes from 600 will fit)
The Air box cover (air filter is identical and worth fitting a K&N one, part number YA-6098)
The front of the air box and rubbers attaching to Carburettors
The Front Brake callipers and pads. (Discs are the same)
The Alternator ( Alternator and rotor from 600 will fit but you would need to change the plug on the connectors
The CDI unit
Intake manifolds (They do crack and leak and are about €40 each to replace)
Clutch basket and plates (A complete clutch from the 600 will fit.
 
The Oil Filter (same as 2002 to 2005 FZS1000) The 600 filter will fit and appears to work but is not correct.
 
The headlight bulbs are like H4 but you need to cut off two of the tabs to fit them
 
A good site for checking availability and prices using the part numbers is www.cmsnl.com
 
The centre stand of the 600 will fit straight on. The chain and sprockets are smaller in width but it is possible to fit the chain and sprockets from the 600. The front sprocket on the 400 has 14 teeth whereas the 600 has 15 teeth.
 
One thing to be aware is the front sprocket nut, it can fall off due to fretting of the threads in the nut and they wear away completely. However Yamaha upgraded the nut (appears to be a very well kept secret) and this is the part number for the lock nut kit 90891-10124. It is advisable to use thread lock when installing the nut and tighten it to over 70 NM. The drive chain slack should be 30 to 45mm and is easy to assume it is slack and over tighten it. If you do not have a centre stand sit two people on it when checking it. If you have a centre stand push the chain up against the rubber chain guard on the swinging arm and it should just touch the rubber on its tightest point.
It is worthwhile replacing the rear shock as the original is very soft with no damping and the fork springs. The 600 replacement options are a straight fit. 
If you have a problem with the lights being dull there was a recall on the 400 to replace a relay and fuses. If it was fixed there will be a circular sticker on the frame headstock with 500 written on it. It may also be the original bulbs as were 60/35 whereas all European H4 bulbs are 60/55.