It's not just gearboxing, the P-38s (if I recall right) had different crankshats among other things. They were convertable, but it was not just a simple swap of parts. It took some work to rebuild them to spin the other way.
When you consider that many twin engine designs flew and fought with co-rotating props during the war, the one-sided torque was not the deciding factor -- as much as the typically diminishing returns on performance as compared to single engine fighters.
Co-rotating the props meant less work, less reliability, not really much benefit gained for making them counter-rotating. So basically the P-38 was the only (don't kill me for saying this if you think otherwise) "successful" counter-rotating design of the war.
There are also downfalls to the counter-rotating props... you could not reduce one engine, then reduce the other without first bringing that first engine back up to the level of the other. At least on the P-38, that is. So each design is not perfect.
Plus, all throughout WW2 engine design, teething problems, and failures during testing of new planes, were the common thread. Poor construction, lack of understanding, or bad manufacturing processes were rampant. Just getting the thing in the air with both engines running meant (usually) relying on an engine you already trusted.
