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Stock TW JB ROMs can use Garwynn's kernel with recovery, version 0.4.1 is CWM and version 0.5.0 is Agat revovery. TW is not limited to only Agat recovery, though the recovery has to be packaged with the kernel on this phone. Right now there are two kernels that will properly backup and restore TW JB and those are the recovery kernels developed by Agat and Garwynn.
As far as custom ROMs go, it is a matter of preference as to what you want the ROM to look like and how it operates. The TW ROMs do have the advantage of being easier to do maintenance updates to PRL etc. Custom ROMs offer other features that user like.
If you are just looking for a look and feel change, then the easiest method is to just try out a different launcher.
What are the 2 kernels you speak of? I would like to try them