Mate in my experience these types are very sensitive to discharging once they have been allowed to go to less than 12v they never really recover and go on to just discharge faster and faster until they fail.   
 
If you want to stick to using the type make sure you use AGM type see here http://www.mdsbattery.co.uk/shop/productprofile.asp?productgroupid=2064&model=FZS1000+Fazer+01-05&brand=YAMAHA&departmentname=Motorcycle+Batteries&departmentID=155  I've used this lot for years and had good service, whatever you do DONT buy cheap Chinese rip off's.  Better still use the older sealed lead/acid type they last for years if looked after and are far better at taking discharging/recharging regardless of all that's claimed I've had to replace many an owners gel type!   
 
You really need to ensure that the gel type is not left for longer than a couple weeks at this time of year without being trickle charged or you will end up deep discharging it for any battery this time of year, possibly to a point it can't be recovered.  Even a good quality low drain alarm will discharge a battery within a month at this time of year when temperatures go below 10* the effect on batteries is quite marked, go further below 5* (probably most nights) and it increases still further the lower the worse it gets.   
 
Keep it on the optimate    or ensure it's charge every week.

Thundercat is a totally different engine especially the top end all be it they share certain internal parts with the Fazer, R6 everything is different.  The carbs from either will not fit without serious mods it would be easier to fit the whole Thundercat engine    and that alone will be a serious bit of work which wont be worth the effort.     Fazers dont really respond to tuning without spending serious money stick a K&N in and fit a good set down pipes/end can they run much crisper and give a few more bhp in the mid range.  They do however respond to handling improvements the standard shock is crap and the front end needs stiffer springs and a play with the oil once done they go much better allowing you to use what power there is lets face it most can't use what's there as standard this side of a race track .  Once done with a good rider on they will stick with just about anything in the twisty stuff or in normal town traffic.
 
Crabs being bored thats a new one never heard of that!!!

Fitted new barrel. pistons and head. Triple checked timing.
Put the rest of it together. Can I get it to start? Can I f#ck!
What is most common mistake a hobby spanner monkey like me gets wrong?

What bike/engine and what was the problem in the first place ect?

Alpinestars tend to be wider that said some of their designs are much wider than others.
 
I have very wide right foot and always struggle with any kind of shoe/boot golden rule always try on as many different makes as possible, I've even found the same make and type of shoe/boot can vary wildly between pairs.  If there tight when you try them chances are they will not loosen much after wear this is due to non natural materials being used now days.   
 
I recently bought Alpinestars SMX-Plus boots I bought half size bigger and just wear a thicker sock they fit perfectly best fit I've ever had. 
 

K & N cleans it up very nicely   

Hmmmmm, well, no. It just went as I was accelerating down the slip road to join the M27, it felt like a misfire but with considerably more mechanical noise. 
 
No warning, just let go, engine never over revved although had 80 000 miles on her. Other 3 still sounded sweet

Have you had it from new/low mileage, how long/mileage have you had it for?

Restore it these are now very collectable not as much as the 650 but still collectable, dont tart it up it will greatly de-value it. 

Mate these can be troublesome at times are you sure you have stated to correct model?
 
I say that as a lot get it wrong and most get the 351 and 357 mixed up they operate differently look here http://metasystem.co.uk/index.php/msy_eng_en/MSYUK/Motorcycle-area/Operating-Instructions
 
From what you say I think the alarm thinks an attempt has been made to remove the battery and it's doing what it is supposed to i.e. immobilising the bike.  What you need to do is reset the unit from memory and this could be wrong its been some time since I did this, on the 351 you need the reset key, on the 357 the pin code.
 
Give the guys at Meta a call info on the link     

Roger that can see now.

Are you saying an MOT station passed it exactly as it appears in the picture?

I'm a bit lost here if the sprocket was fouling the clutch release there is something very wrong why not repair it?  The mod you have done is illegal and will fail an MOT and if your stopped by plod a possible ticket with a strong likelihood you will not be allowed to continue to ride the bike.   

No idea what the cost is but if any part is worn you need to change BOTH, if one carb has worn jets just change all of them. 

Stop smelling it and ride it 
 
Unless it really bad and your fuel comsumtion goes up and/or it starts mucking about for get it and enjoy it.