You have a good list but i would strongly recommend port work and maybe some cpi pipes. The cpi pipes would throw you over budget though. T5's are all around good pipes but for dunes you will be all the time in mid-top rpm ranges. However, do NOT get cpi's unless you are ported to match them. They suck on a non-ported engine.
Portwork is night and day buddy. And since you ride dunes, imo, that's a must. And you dont need a heavy duty clutch. Tusk used to have a clutch fiber/disc set for $40 if i remember right. Elka shocks are top of the line. No need to get something that expensive imo. There's cheaper alternatives that will do you fine. You can also get your head milled for about $40. That's cheaper than a cooling head. I do own a NOSS head and love it but i'm just trying to save you some money man. Only problem with a milled head is you can change the domes(compression). But that shouldnt be an issue unless you know in the future you will run race fuel. You pretty much want the most compression w/o detonation.
As for suspension set up, i cant answer that. I just like going fast in a strait line