Ugh. I've been dealing with this lately too. I just put on a set of strings over the weekend and despite the fact that they were built to Hoyt's exact specifications on the tune chart, it turns out that most string builders build the buss cable 1/16th to 1/8th short and the control cable 1/8th long because Hoyt's specs are known to be off for a good number of their bows. If your harness is built to Hoyt's exact specifications like mine were on their tune charts, your top cam will most likely be at least an inch behind the bottom cam for cam timing. If that is the case and you are determined to make your new strings work, you will need to do the following:
You have to take out as many twists as you can from the control cable and/or add twists to the bottom of the buss cable to advance the top cam. If you run out of twists to take out of the control cable or can't add any more twists to the bottom of the buss cable without making the twists bunch up, you may have to add equal twists to each yoke leg to get the cams in time. Then run an arrow down the side of your top cam to make sure the arrow starts to intersect (without completely crossing) the string at the nocking point. This sets your top cam for proper pre-lean with a center shot set at 13/16 plus or minus a 1/16th. Make adjustments to your yoke until this happens. When you are all done, you'll most likely find that the measured AMO draw length is now nearly 1/2 inch long and the bow under stated draw weight by about 2-3 pounds. You won't be able to twist the string up enough to take up the extra draw length, so you are better off moving down to a 1/2 inch smaller draw module and adding two twists to each cable to bring your draw weight back up. Fine tune everything with bareshafts and yoke tuning to get everything perfect with perfect arrow flight.
In the end, this is what I did and wound up adding 5 1/2 twists to the buss cable and yokes to get my cams timed correctly, plus an extra two twists to the yokes and control cable to get the poundage up, plus moving the mods down a 1/2 inch. That is 7 1/2 twists total in the buss cable and yokes and 0 extra twists in the control cable since I added back what I took out. If 2 twists equals 1/16th of an inch, then I had to adjust my cables nearly a 1/4 inch. Ideally, you would want that much adjustment spread out over both cables in order to keep the DW and DL in spec. One email to my string builder the next day and several going back and forth from him on exactly what I needed over the weekend and I got myself a replacement set on the way under warranty. The new set will be 1/8th short on the buss cable, 1/8th long on the control cable, string built to spec, and when installed I should be a 1/2 twist from perfection.
So.....long story short. Keep track of what changes you make to your new harness. If things end up out of spec, contact your string builder and let them now.