Reddit mentions of Yamaha FZ6 Fazer '04 to '08 Service & Repair Manual

Glad to see you have the faster blue fz6 as well!

First recommendation, buy the Haynes manual! It will come in handy if you plan on doing any work yourself!
Also check out the boneman's mods here. He was an active member of the forums in the past I guess, and though his mods were for the older gen fz6's they are all still pretty relevant. It's a good place to get some ideas!

I'm almost at 28k miles on my fz6 and it's running great. Just did the valve service myself this last weekend and that is really the biggest maintenance you've got to worry about. A common issue I've seen on the forums is the steering head bearing wearing out quickly. It's pretty easy to check, just put the bike on it's center stand and put the front wheel in the air. Then, turning the handle bar all the way side to side and feel for any resistance, it should move very freely, any resistance should be pretty noticeable. Also, with the front wheel in the air, if you grab the front and back of the front tire and move it back and forth it shouldn't be loose feeling at all. If it is, the steering head bearings need replaced.

Since nobody has said it, maybe the clutch and throttle cables could use some lubing. When I bought my fz6 the clutch cable needed it badly. Make sure to clean and lube that chain too.

I would disagree about K&N air filters, some reading on the fz6 forums made me against them. Just that they have wide air gaps that filter less which is why there is supposedly a slight improvement in power, but you're filtering less... which is not really good because you don't want junk in your engine. But anyway!

Possibly replace the spark plugs too. Or at least check them and make sure the gap is in spec.

I would get some frame sliders quickly just in case. Motivation is supposed to be the best, according to webbikeworld and is what I've got on mine. Plus you can rest your feet on them on longer rides.

Depending on what you plan on using the bike for you could get some Givi hard cases. I've got a givi top case with the leather padding, great for carrying stuff and my girlfriend is super comfy and feels much safer with a rest.

I could keep recommending mods but that isn't what you asked for so I'll stop :)