Just a quick thought; as you've disconnected the battery, your ECU may have lost its 'auto adaptive parameters' (have a look here for more details -
http://www.ukmonster.co.uk/monster/s...ad.php?t=55198).
If that happens, then it may manifest itself as rough running at lower speeds and you may find that the tickover hangs at around 2k for a couple of seconds before dropping to normal. Don't worry if this happens; the self-learning part of the ECU will sort it out within a couple of hundred miles or so.
No one seems to know how long the ECU can hang on to this information after being disconnected from the battery; it could be minutes or hours but I thought I'd mention it in case you feel any difference when you ride it again.