Cylinder/Piston - Your options on the Wiseco are buy a complete one from Lancer....or get it done yourself. Lancer uses Boretech to do the boring and Silicone Carbide treatment.....and the owner is a full time cylinder boring guy, a biker, and a nice guy. If you have him do the work you know it will be done right the first time. So many shops just don't do enough boring to be really good at it....I don't know of any others that do the Silicone Carbide Treatment. You can buy a piston off eBay and have it shipped to Boretech, ship him the cylinder and have it bored and the Silicone Carbide Treatment applied....you will probably save a bit of money over what Lancer charges. Lancer has to pay for shipping to and from Boretech to where he lives and then on to you....so his cost in preparing the kits will be a bit higher than what you could do if you want to take the time. (If the shop gets the boring wrong and it is too tight....the piston can seize in the cylinder. Too loose and it can rattle and burn oil).
Carb - I have a 95mm Wiseco on my bike and a 34mm Mikuni. It is all the carb you need on the bike, and the smaller size makes the idle and cruise operation better than the larger carb would. Once again you can buy the carb from Lancer and he has worked out all the jetting and parts needed for the installation.....or you can shop around and piece it together yourself. The 34mm carb jets can vary greatly as some are jetted for 2 stroke bikes when you get them. You will need a special throttle cable for the installation, along with a different rubber adapter/clamp at the cylinder head.
Header - The stock header works OK....but a larger one would be a bit better for performance. Currently no one makes a 1.5" header - so you will have to have that made on your own.
Muffler - A straight pipe is not ideal for good performance. You need some form of baffle inside to cancel the pulses in the exhaust flow. It does not make much sense to improve the performance of the engine with a new piston and carb, and then lose those gains with an open exhaust system. The DYNA may be a bit too restrictive for a modified engine - the EMGO muffler would work - but it really needs some changes in the baffle to reduce the noise. I plan on doing a Tech Article on that this summer.
https://www.youtube.com/watch?v=KjKUKhHQLHgAIR BOX - The stock air box works just fine on a modified engine. The cylinder head is the biggest restriction in the performance of this engine, and the air box can keep up with the flow the engine needs. The cone filters are not all that great in flow - they are just easy and folks that like the "simple" look prefer them. The stock air box is waterproof and works just fine with a modified engine - I suppose if you tuck the cone filter back behind the battery box and between the side panels it will be more resistant to water getting in - but if you just hang it on the back of the carb any water that reaches the filter can go into the carb and/or engine. Removing the stock air box is a lot of work.
Gearing - The Kawasaki pulley conversion is the easiest way to keep the belt and change the final drive gearing. You can change the front pulley without any problems with the belt fitting - or you can do both pulleys.....you can't do the rear one alone without making the swing arm longer. Harley pulleys and belts don't work....they are narrower and the teeth are round instead of square.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1384949185Forward Controls - I don't know anything about them....there are a few vendors in the Marketplace Section.
Fork Replacements - A few have done it, not sure what you mean by a "better set". It is not an easy conversion as often the front wheel, brakes, fenders all have to be changed if you try using the stock fork yokes....and likely the fork tubes (38mm) won't work with the way the top yoke is attached to the fork tubes using the fork caps. If you change to the fork yokes you have to adapt the forks to the steering stem and bearings.....and often the trail changes and can make the bike steer sluggish if you increase the trail.
Rear Disk Conversion - Some have talked about it, a few have done it. It does require a lot of work including a change in the rear hub. Not really worth the time and effort, as the stock brake works just fine and never wears out.
Cylinder Head and Cam - You did not mention either of these, and if you are doing work to improve your performance there are some noticeable gains here. The ring at the end of the exhaust port can be trimmed down a bit, and a fit of smoothing of the ports can be done o the cylinder head. The cam needs to be changed to a performance cam - for cruising around the Stage 1 or Stage 3 cam are fine and do a good job...the Stage 2 cam is the most performance oriented grind.
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