Are there any engine differences between the 03/04 vs. 05/06 VQ35DE non rev up?

Mostly on paper. The 5AT "sedan" 03/04 was rated at 260/260 where the 05/06 was 280/270. Dynos have shown that there is actually only a couple hp/tq difference between the two.

I read in some of the press releases Infinity was claiming stronger, beefed up engine parts when the 05's first came out? Is that only the rev up?

I believe so. The rev-up has a number of changes besides the timing like a better oil pump, etc.

They were also claiming that the 280 horse engine had VTC on the exhaust side. I checked this weekend and found that on the service manual for the 2005 sedan it does mention exhaust VTC but only for the 6speeds. Auto cars only have it on the intake side.

Yeah that's only on the 6MT (rev-up) engine.