OK
Denver, ~5K feet. Air pressure is lower, cylinder pressure is lower. The FatCat bagger pipe has an inherent torque dip in the 3,200 range not too bad though and it has strong torque above and below that. The air pump sucks, the heads say go go go, the cam says slow down a little, the motor goes to get a breath and only gets 24.6 VS 29.9 pressure and this affects power and torque in all the operating ranges.
Based on this I always recommend builds at altitude to use smaller cams, higher compression (but not over the edge for sea level operation), and pipes on the smaller side when given a choice like you have here. The result will be nearly no loss on the top and better low speed torque, something you will notice all the time just running stoplight to stoplight or doing the famous "pass a truck" scenario.