The first issue was that 4.1 didn't want to boot from the new pendrive. Assuming I did something wrong with the imagedd.bz2 file, I tried it a few times more, wasting about 3 hours. Turns out the box didn't like the Veritech pendrive somehow. Running from a Silicon Power one went like a charm.
Second issue: the LVM.resignature config option disappeared from the ESXi advanced config. Our new friend is the esxcfg-volume command-line utility.
Use
exscfg-volume -l
to list the volumes, and
esxcfg-volume -r
to resignature (and rename) your volumes.
On a related note, ESXi 5.0 does not use the imagedd.bz2 file anymore, so I didn't even start to experiment with it (I wasted too much time on trivial stuff during the upgrade anyway).