1. Modern wheels with similar rims (graphite or black) pictured above with.....red calipers
Easy to do. Just find a wheel vendor with the style and spacing you want, and your in business. Enough guys on here have moved to 17" wheels that you just need to pick their brains for sizing choices and make the call. Red calipers are as easy as caliper paint from Plasticote. Find it at your local auto parts chain store. Or, if you want really get trick, a Viper caliper kit can put genuine RT10, four piston, black Viper calipers on 11.75 brake rotors for modern braking force and feel without radical modifications. This would cost you in the neighbohood of around $700-800. Or if your going to 17" wheels, you could put on 2nd gen, red Viper calipers with 13" rotors for the ultimate in stopping power for around a grand.
2. six pack hood and on the side of the hood scoop I want to badge it as a 426 hemi
It's you car, man, if you want to call it a Monoco and put the 6 pak scoop on backwards, its your business. Of course badging it as a Hemi means people will ask and then you may have to explain or shrug them off. See below for more info.
3. All trim in black
Another one that is not too hard to do. Anodizing or coating the pieces is the most durable way to do it, but you could paint them. Another trick you don't see too often and now that your paint is down it is too late to do, is shrinking and raising the windshield and backlight openings just enough to flush mount the glass and ditch the trim for a gasket is one of those subtle, but noticeably different things between old and new cars.
4. Front grill painted totally black with "an improvised" but removable black plexiplate that makes it look like I have hidden lights (for show only, I'll remove them when I drive it). should make it look REALLY mean.
This is the toughest thing you have on the list. I have been looking at ways to convert my stationary light covers to moveable covers and there is no easy way to do it in a way that leaves them flush to the grill in the down postion or fully hides them in the up position. Right now mine are easily removed and I only put them on at track events. I anticipate I will need to also change the grill to more of a flush mounted set up once I can get a mechanism that works mocked up on my car. Scroll my avatar over to see the front end with the covers installed on my '74. It is VERY tough looking, IMO. If you want to look at different materials check out the mcmaster carr online catalog.
5. Tinted side windows.
This one is easy. Just take it to the tint shop and have it done. Looks great.
6. Challenger emblems - try to paint red (not sure)
There are enough reproduction badges out there that you can easily paint these red, either completely or just the centers to give them chrome trim, but that may clash with the rest of your black trim. You also can find enough repop badges that you won't need to put Hemi badges on something that isn't a Hemi. Because of the demand, Mopar makes badges for 318, 360, 340, all big blocks, 4 bbls, 6 bbls, or almost any combo you can think of. Go here;
http://www.mopar.com/performance/muscle/index.html and open the catalg. Then open the restoration tab, then open decals and badges and take a look. Your local Dodge dealer can get you any of these. There also is the option that you could badge it something else that didn't ever exist. R/T/A, Challenger GTS, R/T8, or something like that. A friend of mine with a Demon adopted the Viper snake logo to his car and added the demon horns to it for his build up. Looks neat and different. Get creative here. If you really want metal badges, there is a company called Car Jewelry or something like that who can custom make any badge or logo you want. You also can spec almost any type of decal and have a local graphics shop cut them out in vinyl to be install on your car. Crossbreeding other badges such as the Magnum V8 badge found on trucks through out the 90s or actually using Viper stuff is possible too.
7. Bumpers black - Can I do this?
8. Valence graphite
9. Fuel tank graphite with black supports.
Yup, just scuff and shoot like any other body work. Don't forget the bumper bolts though.
Overall, love the theme and like your vision. It is coming together nicely.