Is it necessary to have both hot ends on a dual extruder printer at the same height?
I have a dual extruder Replicator 1 and having the nozzles at the same height is a must and albeit a bit of a struggle otherwise. At one point, I had to disassemble my extruder head and the nozzles didn't line up quite right. There after, printing with the lower one obviously didn't have any troubles, however, printing with the high extruder made it so the lower extruder would scrape the molten plastic layer. This made my surface finish horrible and almost impossible for support structures to be printed.

Instead of fighting with my stock nozzle assembly to get everything perfectly lined up, I just shimmed the one side with some stacks of paper cutouts. This brought my extruders very close to even.

Also, you'll want to make sure excess plastic is cleaned off of BOTH nozzles when printing with either nozzle. I found that some prints would fail because of a small discharge from a previous print on the other nozzle.