Jason at wakemakers suggested to me that is can be hard on the pumps if they are running at the same time. This spring I did the reversible pumps mod, and will say the putting in two new thru hull fittings was the easiest part of the job, it really was, and after spending near 200 bucks on each pump I thought why risk ruining one. It really took me 20 mins to drill the holes and install the fitting and ball valves.
Jason told me that for the small cost it was worth it to put dedicted thru hulls in for each pump.