1. Should padding be in the shorts or the saddle, neither, or both?
less padding on the saddle
more padding = more discomfort on an exponential scale
saddles are like shoes - do NOT buy one without trying it for size - see this thread for athe specialized solution to measurement
http://www.bikeforums.net/showthread.php?t=242143
using the pelvic measurement tool in the thread linked as a starting point for saddle choice take the bike to the bike shop and switch out saddles until you find one that's comfortable
well made padded BIB shorts(bib becuase regular shorts make me feel like I'm being cut in half)
generally more expensive = better but mine are mid range and quite comfortable
as with saddles too much padding is a bad thing and seams in the chamois/padding can become very painful on even short rides
2. Should I get a gel saddle? something like a specialized toupe gel, avatar gel, milano gel, ect.... Should I get padded shorts? Are they all padded or only some?
as above
3. As far as shorts go. I have never seen so many different types. I dont even know where to start. What is a good company to start looking for. I am a 42" waist so I dont know if all companies will have my size. Whats a good material? I see 6 panel and 8 panel? All different styles of chamois' too. How does the sizing usually run?
more panels = better fit
bib shorts = all day comfort
artificial/synthetic chamois or man made pads are better as I hate the feel of a lubed up real chamois (mmmm, chamois cream......NOT!)
I did some research and these are really the only ones I have found. Are they any good? any recomendations on a specific short?
go with what feels comfortable
that is, as with the saddles try before you buy