D66 for your early 99 will be just fine. I loved it when I had mine. The only reason I took it off is I wanted more power. I made 471hp with my D66. It towed awesome as well. 20mpg when empty as well.
the only reason to upgrade to a late99-03 system would be to go with a Garrett GT38R turbo or a TN BB and it will only make as much power as I did with the D66. The GT38R is good for 450-475hp. The D66 will get you there for less than the GT38R alone. To convert you need up pipes, pedestal, turbo, intake "Y", intake plenums. You will need these parts here:
http://www.dieselsite.com/index.asp?...ROD&ProdID=276
and then a turbo like this one here:
99-03turbo
So, if you just use the basic prices that are from the sites I listed above you get $700 for conversion parts and $1850 for a turbo you tie up $2550 plus freight.
D66 is $1325 plus freight. One hell of a deal if you ask me.
Another option would be a Hypermax H2E. Cheaper than the conversion and the future options are endless.
Keep Strokin'