The software I use (Autopano Pro and PTGui, depending on application) seems quite forgiving in that respect when it comes to daytime shots, though I do plan my overlaps to minimise potential problems.
Nighttime is a different story because of the longer exposures. The first of the photos is actually a HDR made up of 33 separate shots, with up to 20 seconds each. I shot about five sequences until I got one with minimal boat movements. Took about 2 hours all up (including a few other combinations), with intermittent showers ... being patient definitely helps.
slt

