Not sure where you heard that 1999 - 2000 where bad 7.3's. Yes they made improvements through till 2002, but those are still really good motors especially because they used forged rods in those years. In and around 2001, they switched to PMR's and that severely limited how much you could mod them. The PMR 7.3's are limited to 400hp whereas the 99-00 you could mod to beyond 500hp safely. If you want a good stout towing motor, stick with the 7.3. If you want to go fast, go with the 6.0 but stay with 06-07 MY's.
2001 F350 CC SWB 6spd....currently getting a complete 'makeover'. Stay tuned.