I'm just taking a guess, but did you move the loop down the same amount as the rest? If so then your tune shouldn't change much, but you also have to move the peep down a like amount. This may be the reason your anchor and comfort is all screwed up.

Also, don't know how the loop was set before, but the inside of the top knot should not be level with the rest. It should be approximately 5/16" above square to compensate for the arrow diameter. Start there and retune.