Simplest way is trying to match equal length but if you can get flow rates matched (shorter pipe having a slightly wild bend creating slightly turbulant airflow) you have even closer performance for each pipe (fluid dynamics class helped out a bit with this, but some drafting programs like solidworks i think figure it out for you). I would try to avoid stepping the pipes too much though just because of the asthetics, needing multiple sized tubes, and 2" pipes are plenty of volume (I ran 2 1/2 on a corvette with over 400 hp no issues) unless your taking your bike over 100 hp its kinda wasted metal and less back pressure which people often overlook for helping generate torque and also helps the engine fire so starting cxan become difficult.
What i would do if you want bigger looking is to put a wider tip on it or do angled cuts. To balance it you could do a 2-1-2 pipe design like the bike originally had or a 2-1which would help compensate for planning oversights.
Also programming units usually are set as a table combining averages for the whole engine, not each cyl. when they get modded there are bumps you make through certain ranges in Throttle position and RPM for fuel, and timing compensation or step the entire table. which means you cant tune individual cyl's
Also dont forget to consider the exhaust is exposed so you need a nice finish on it (chrome or powder coat so check those prices to factor in too) these arnt sport bikes or dragbikes so