N55 is the 2011 sedan and 2011-2012 coupes. N54 is every other 335i including the 335iS.
Regarding the N54 vs N55, the N54 will be able to make more power with a tune versus the N55. The N55 is more reliable and won't have as many issues, but if you plan to tune you won't make as much power and will need to upgrade your charge pipe. The N54's major issues (Turbo Rattle, whine, HPFP, injectors) are now all covered by an extended warranty that is seperate from the factory/CPO warranty though, so I wouldn't let that steer you away.
MT jerkyness? I doin't know of any, but you should be doing the CDV delete right away if you get a manual.