If you are having the same problem as me I honestly don't believe this is a problem on our side. FFXI doesn't just randomly start running into problems where after a year of running fine, and also the fact that a bunch of people are having the same problems (who happen to all use nvidia cards) shows that it's most likely a problem on the server side of things. So I wouldn't go running off to buy a new power supply or video card or program to optimize performance (unless of course you just happen to want one of the previously mentioned items) just yet, wait and see what SE does if they are indeed working on a fix for this upcoming version update as you said.
I'm not quite sure when this started, but 2 people in my linkshell, both nvidia card users, have both reported the same lag spike or choking as you call it where the game freezes or locks up for a few seconds then proceeds to go back to normal. This happens to me most often when I go to start a battle as I'm fighting in a zone such as sarutabaruta.