If you're mechanically inclined, everything you've described shouldn't present a problem. For the header mods, I recommend doing a search, this question has been brought up frequently recently. The header mods won't require jetting changes, stock or modded.
If you don't remove the airbox lid, or cut holes in it, jetting probably won't be necessary. Otherwise it will.
Hope this helps.
BTW--What elevation are you at?
2000-440ex Stroker--Fan Cooled
Houser +1 A-Arms, Elka Triple rates, Laegers +1 1/4 Swingarm, G-Force Axle w/Durablue Anti-Fade Locknut, 14/36 Gearing, DID X-Ring Chain, C&D Revalved Rear, Maier Silver Plastic, Steel Grey PCed Frame, SPAL Fan, AC Bumper, Pro Armour Footpeg Extensions, Renthal Bars, Yoshimura Full Exhaust, 450R Carb w/ZR's Adaptor, K&N w/o Lid, Powroll 440 Stroker w/stg 3 HC, P&P Head, HD rod, GT Thunder HD Studs, and Timing chain, AMR Monster Coil, 4 Degree Advance Key and a 12oz lighter flywheel. Now at 12.5:1 Compression!
450R Front brake upgrade using 06-up Spindles and 07' hubs.
450R Rear Brake Upgrade
Kenda Knarly XC Radial 21x11x9 Rear Tires
Shorai Lithium Iron Battery
Running E85--Jetting: 70 pilot, 240 main, HRC needle on bottom notch and shimmed.
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