Certain footpegs from the now defunct Buell can be fitted, about 1.25 inches lower.  That and a higher, re-foamed seat might do the trick

Also remember that the FZS600's fork inners were updated because the 2000-2003 forks had preload caps added compared to the original 1998-99 forks with no preloaders. This probably would have forced a change in spacer length.
According to my service manual, the '98 bike has a fork spring free length of 323mm and the spacer 200mm
 

Hi Vinny,I would probably still opt for the 15w oil: using 10w might cause the forks to rebound back up too quickly, unsettling the bike.  I suspect you think it'll need a lot of tweaking, but you might be pleasantly surprised - providing the valve's preload is set up just right for you, you may not actually need any adjustment bar possibly adding a little more fork oil to each leg.
That spring rate should be about right for you: the ideal rate for our sort of weight sits between 0.85 and 0.90. Again, adding 10ml of oil will firm up the final part of the stroke, which would stop the fork bottoming out if needed.  Using the cable tie round the stanchion for measurement, you should be aiming to have about 10mm of unused fork travel under road use.

I already had a Micron front paddock stand from a previous bike setup, but you could either:

• Put axle stands under crash mushrooms (if you have them fitted), or:
• Use the jack with a block of wood under the pipes.  Although not my preferred option, I believe plenty of others have used this approach without causing damage.

Vinny,Unfortunately I only ever fitted Racetech and Debrix fork emulators, never had my hands on the YSS ones so am not sure if they're exactly the same  Those other Emus called for 2.5 turns of preload, along with 15w oil.  I never found them overly harsh even with the heavier fork oil.
Re: airgap - my '98 service manual says standard fork oil height is 121mm from the top of the fork (with springs out and compressed).  I am not sure if this changed for the revised forks from 2000 onwards.  If you have a 1998/99 bike, I would try reducing standard height by about 10mm (so a 130mm gap) and take it from there. Put a cable tie round the stanchion to see how much travel you're using up.

For the full lowdown on YSS valves, you could try sending a PM to 'Tommyardin' as he fitted YSS emus to his forks and got a great result.

I think the the 2005 bikes had a CAT fitted inside the exhaust system.  I'd assumed it was in the rear half / tailpipe part, but perhaps its actually in the midsection of this part?

Bargain....

what is the length of the standard forks, from the centre of the axle to the top edge of the fork cap.

It's about 810mm, and unfortunately I also have uprated springs in mine.
 Most importantly, they have 140mm of travel. With the rider on board, you're roughly looking for between one quarter to one third of travel being used up. One quarter of travel (35mm) will feel firm-ish, one third of travel (46mm) will feel soft. You could go even firmer (down to 30mm) but wouldn't go softer than 46mm.
I put a block of wood under the exhaust pipes, jack it up and then measure the length of exposed stanchion from underside of yoke down to the fork seal.  Then off the block & measure again.

As an alternative, I'll soon be selling a pair of new Racetech compression valves (somehow I ordered two sets from the States by mistake). You essentially bypass the fork leg's external screw setup as you tailor the internal valve shimstack to your own weight (comes with a Racetech access code). They cost me about £180 inc import tax but could let them go to a fellow f0ccer for a bit less. Obviously tracking down a trashed pair of forks would be a cheaper, but you're stuck with the mediocre damping.

My own forks have these fitted, as well RaceTech's rebound valves: haven't felt the need to adjust anything yet and I'm probably a bit fussy when it comes to suspension 
Guide here:   http://www.yamahafz1oa.com/forum/showthread.php?t=67950
& here (for FJR1300) which shares the exact same valves:    http://www.fjrforum.com/forum/index.php?showtopic=127506

Good work 
I think because dealers use mileage as a bargaining tool, many of the bike buying public has been persuaded that a bike is for the breaker's yard beyond 20000 miles     

You only have 222,000 miles to go to beat Denise Dickinson on her 2001 FZ1
https://newsok.com/article/3661565/oklahoma-city-woman-hits-200000-miles-on-her-motorcycle

http://www.yamahafz1oa.com/forum/showthread.php?p=2709899

I've heard of people squeezing 1200 engines into Bandit 600s, but I don't think it would be quite so easy with the Fazers
Normally I'm all for mods, but...... 40+ more ponies into a 600 which was fairly budget in terms of frame & suspension setup?  Surely the engine bay within the 600's frame would be too small & there'd be no room for any sort of airbox (or even filters)?  Engine mounting points around the frame would also differ both in position and diameter on the 600. You might need to bore them out, which would then reduce the structural integrity of the frame. The 1000's radiator is larger (and needed - you couldn't run it with the 600's rad) and therefore likely to be hit by front forks under braking. 
I suspect the basic steel frame & aluminium swingarm would be very borderline at coping with all the extra power and torque and the standard forks can't even cope with the standard bike's performance.

...but if you do decide to go for it, and have very deep pockets, keep us all in the loop 
Personally, I'd have considered 660/695cc big bore options for the standard engine: that would provide a more realistic boost for the chassis. Or just go nitrous and get a heavy duty clutch fitted.  Or just buy the 1000 

Great news, well done! Hope you get her fully sorted 

Not an absolute indication, but if you look at ebay through the 'completed listings' filter, you'll see that the highest priced bikes aren't shifting (and have been on ebay for ages with repeat auctions). The ones that have sold appear to be in the £1000-£2000 region, with the very occasional minty exception.

Like most people on the site I feel there's nothing that comes close for getting on twice the money they're currently valued at (I quite like the new Versys 1000 but not really *that* much of a quantum leap forward and £7,000 upwards).  The best 1 litre all-rounder with oldskool carbs will eventually regain it's true value...

When you own one, it's worth next to nothing. They're completely valueless once the second big valve service is due.
When you're looking to buy one, it's 'a future classic' and worth two or three times as much. Either that or they are 'too old for the showroom' and broken on ebay.

Despite a few people saying they'll go up in value I fear think they might be similar to early Honda VFRs: pundits argued that as a great bike they would inevitably balloon in value and yet to date they haven't