I am running 2" Hooker Comps and and I haven't noticed any issues. However, I used ARP studs on the heads and because of that, I had to grind the header flanges around the studs to allow them to fit properly. I also had to move my brake prop valve to the top of the frame and was able to reuse my existing brake lines.
As far as the crank seals, I think you will find everyone has different preferences. Though I just went through a rebuild which included a new crank, my rear main is leaking. I used a Felpro seal but for some reason it didn't seal properly. I was going to do a little research to see what's out there, maybe go with a viton seal next time?