I actually don't hear about it more than any other truck. But.... I think the fuel filter/canister design is poor. It's kinda pointless since they'll basically let bad fuel and junk through. Then the dealer sticks you with the bill.

Moral to the story, keep your receipts and records.

 

I think you could find a good 03/04, low miles, for 15-20k. For work, perhaps auto would be better?
If you use it for work, I am not sure you would want a lot of mods.
The 6 speeds are great, if you are towing. Around town, they can get old.