Off the bat the only thing I recommend changing would be the saddle. The LHT I bought was a 2007 or 08 so I don't know if they changed saddles or not. I just didn't find the stock saddle comfortable at all. I just ordered a Brooks flyer and hopefully will get it soon.
I have the 54cm LHT and they have the WTB Slickasaurus'. I haven't had a flat yet and I've been commuting on mine since December of 08. I'd wait on buying new tires to see how you like the stock ones first (unless you LBS will swap them out to the Marathons or Gatorskins or whatever for free).
I have not had problems with the rear derailer or the brake pads; so again see how you like them before you decide you want something else. The LBS (not local to me) said the LHT was probably the only bike ready to tour with right out the store as is.
Pedals are your choice. Some like the clipless, some like the flat bmx type, but I have a pair of Wellgo (somethings) with PowerGrip straps and they work fine for me.