Whcih customisations ??
In summary, my upgrade procedures are pretty simple really.
Just follow the normal upgrade procedure making notes about the files that will be changing - These can be spotted by the diff files. - and checking this against those that have been modified.
When going through the upgrade it will try and make the upgrades itself but any fails will be notified in the failure log.
If these are critical to the operation or look and feel of the site then the latest 'fresh' versions of those files are looked at to see how to integrate the mods into those.
In general though, if you have made lots of mods it will fail the upgrade to the template file and therefore you mods wont be lost - just might lose some of the improved functionality of the new version.
Cant say this for sure when 3.4.0 upgrade kit comes out though
