If you are going to modify it, I'd say the CR; I rode DBDave's, which was modified extensively, and was the finest, best thought-out and complete setups I've ever had the pleasure of piloting. Were it not for the close-ratio trans, I'd own it today.
(I had another intermediate vet. friend that bought a new '97 CR when they came out. He gave it a go for almost a year then got rid of it. He hated the harsh suspension, abrupt and mostly top-end power, and vibration of the 1st-gen Al frame - said it beat him up/wore him out. He's a Honda guy too, and a good tuner (does his own suspension). He used it for off road (grand prix, vet MX; hated it for trail riding.)
If you are going to do some simple mods, then go for the Zook; the conventional forks are about the best to come from Japan for trail riding, and in a traditional Suzuki way it will turn on trails effortlessly (most anybody on any bike can go fast on straights). Put on a big tank, spark arrester, skid plate, hand guards, and Steahly fly wheel weight on and you are good to go. If you have some more cash, then add a stabilizer and a good turning bike is not a stable one.