Never ridden a bike with Eric's porting, but I do know in his book he mentions the '99 CR250 cylinder is better for many riders. It has more mild porting, strong low end for a 250, and will get good fuel range with your '97 carb and electronics (mine goes over 70 miles at aggressive trail pace with a 3.2 gallon Clarke tank). Long piston & ring life, too.
The stock '99 pipe is also excellent for trail work. You may be able to swap cylinders/pipes with a '99 owner who races MX, or check the auction site for a deal.
For putting the power down, the e-line lighting coil reportedly works even better than a flywheel weight, as the magnets help to smooth the power. Probably too expensive to justify just for the power delivery improvements, but you can use the power leads for hot grips as well as lights.
Mine has the V-force reed block and carbon fiber reeds. Popular mod for woods riding.
Also, set your sag on this bike at 105mm and get a steering damper!
Bottom line is you can make your CR into a formidiable woods bike but it is going to cost you a fair amount of money, espeically if you add items like an 18" rear wheel.
I bought my '99 from a former district enduro champ (he also won the title on a '97) and it is incredibly good in the woods. Check the garage tab at the top of the page for a list of mods.