I have no idea of the difference between version 1 and 2 of swap partitions. My best guess will be that this have no influence on the speed of LVM partitions. It can easily be changed. Disable swap and regenerate the swap partition using default settings will create a swap partition version 2. Remember to turn swap on again;-)
AFAIK the setting in lvm.conf will only influence new LVM partitions but what is worse seems that this setting is used when creating the PV (psychical volume). This indicates that you will have to recreate your PV before the right alignment is used:-\
If you are suppose to recreate the PV my recommendation would be to start from scratch and then use the defaults. Swap version 2 and alignment of partitions using 1MB which is the default.
That is consistent with my assumptions. My best bet is to create a new system from scratch, with all recommendations from this post. New ones are welcome, of course.
I'll report back when a new system with similar hardware is ready, and this thread could be for reference to anyone.