You will see zero power loss by having your gun a foot away from your chrono, you'd have to be more like 5 feet away to see anything. I have a Caldwell chrono and am able to shoot over it at up to 50m, and you definitely see serious losses at that distance.
As for the inner barrel, I would suggest that you don't change it unless you get a PDI, Faceless(nicer PDI), Lambda, DaVinci, or EdGi, and I would not buy one of those unless you need a 6.01 or tighter. I highly recommend lapping your barrel, it will perform better than anything, except Faceless or EdGi.