I went from a '99 auto to an '01 ETH/DEE and have no complaints at all. I drive in Houston traffic every workday and most weekends, so I have to shift allot but I like my 6-speed. The auto was mildly BOMBed (275's and boost mod, DTT VB) and it was fast enough for me around town. I believe that most of the speed in that truck was due to the auto and not the engine, though. This truck is not as fast around town as the auto, and from stoplight to stoplight it may not be as fast as the 5-speed since there is an extra gear in there, so if hot-rodding around town is your thing then the auto is better suited for that. Out on the freeway from about 50mph on up I believe that this stock truck with only about 700 miles on it is faster than the auto that I used to have. It pulls better in each gear and seems more willing to rev than the '99 did. I have also seen better mileage on my first tank with the '01 than I ever got with the '99. More power and better mileage... go figure.
I have heard guys with the 5-speed say things like "It would be nice to have the 6-speed", but I've never heard anyone with the 6-speed say that they would rather have the 5-speed.
The people at South Bend Clutch are supposed to have the answer to the clutch issue and they are spoken highly of here on the TDR. I put allot of stock in what is said by people that have nothing to gain by offering an opinion.
Can't help with the 4x4 vs. 4x2 question, both of mine have been 4x2. I know myself too well to buy a 35-40k 4x4 because I would drive it places that I have no business driving a 35-40k truck.
You asked about adding power so from my knowledge here goes:
The 01 (and '02 AFAIK) auto has the HY35 turbo which has a 9cm2 (I believe) exhaust housing. You will very quickly run into EGT problems if you add power to this combo and will have to upgrade the turbo. The auto will need attention if you add more power than something like the EZ, VA, or mild injectors like DD1's or 275's.
The '01 (and '02 AFIK) manuals run the HX35 turbo which has a 12cm2 (I believe) and generally does not need to be updated until you add allot more power. The clutch on the 5-speed will hold more power than the one on the 6-speed before slipping.
There are three popular ways to add power to these trucks. They are injectors, electronic boxes, and drugs.
Injectors range from bosch 275's to the fire-nozzles that DD makes for the seriously BOMB infected.
The electronic boxes like the Edge EZ and VA offer modest power increases and can be removed without leaving any evidence that they were there. The boxes like the PE Comp, TST Power Max, et al will require that wires be molested in such a way that evidence will be left behind and can be spotted by DC techs if they look for it.
The drugs are propane and I believe Nitrous but I could be mistaken about the nitrous. I have no real knowledge about the drugs, so someone who knows better than me will have to address this for you.
Hope this helps,
Mike