Been doing more thinking...in no particular order:
A. What route are you taking to get between NY and Chicago? Is Chicago a must in both directions?
B. If you truly have the time to burn, have you considered taking US-2 (and adjacent roads) as your East-West route? I always wanted to do that, but haven't had the chance yet.
C. Pacific Coast Highway from SF to LA is a fun daytrip. I think southbound is the better way to do it.
D. If you spend any quantity of time in the desert, you need REM's New Adventures in HiFi album. It just fits the landscape. Especially at 100mph+, though that won't likely be an issue for you.
E. The middle of the country is boring as #### on the interstate. Seriously mind-numbing. On this account we did the Fort Collins, CO to Cheyenne, WY to Ann Arbor, MI run (~1300 miles of our 4300 mile meandering SanFran to MI trip, if memory serves) in one shot, starting at 11pm after a half-day of hiking on "difficult" trails and 400 miles earlier in the day. It sucked and I would not recommend it. But it probably sucked less than if we'd taken our time to do that section. Either find interesting sideroads to break up the I-80 monotony, or consider a northern or souther substitute, such as my US-2 idea.
F. I've used the same ratty full-size US+Mexico+Canada road atlas for trips all over the country. It provided adequate detail to get you where you want to go, without having so much as to confuse you or lead you onto tertiary or unmaintained roads where you shouldn't be. The state-specific Gazetteers are pretty good for detail, but you can be plenty entertained with the regular road atlas - just follow the dotted "Scenic Route" roads, you'll be a happy camper.
G. Autorouting GPS is really nice, especially for unfamiliar cities. Topo is interesting for places with terrain. Something like my crappy Magellan Crossover + RAM mount would probably keep you entertained for <$200 off eBay.
H. I like Michigan. And not just because I live here. Check out a couple of the threads in the Central States area and completed expeditions section (UP Overland 2008, UPCruiser's trip reports for Whitefish Bay and the Keeweenaw, Haggis' UP trip thread). If you like photography, there is a LOT of good stuff up there. The sunsets and sunrises in the UP have something special to them, possibly owing to the northern latitude. Also consider the western side of the lower peninsula, too, for sand dunes and wineries and stuff like that.
I. Truck stops are fine for sleeping. I've spent quite a few nights at them, usually sleeping semi-upright in the driver's seat. Just pull in wherever, back into a reasonably secure spot and knock off for a few hours. Rather than the dark back corner, I try to park near the lamps, and cover the windows with a towel or sheet.
J. U-joints, ball joints, and steering linkage. Make sure they're good, tight, and well lubed. Vibration sucks. Loose steering gets old real fast. Also make sure that t'case and axle (pinion) seals are good.
Anyway, I'm sure I'll think of more "wisdom", but this is enough for now.
On a personal note, I really do envy you being able to take this kind of trip. There are few things I would love more than to load up a couple weeks worth of stuff into my '02 Wrangler and head west.