I have some websites running on j2.5 while others are on j3.x. Do i need to upgrade them all to the same version before linking them through jms?

We are able to do that with aJmooL and our "legacy extension" that we are finalizeing.
See www.ajmool2win.com for more info.
Currently, most of the material is in french but you have the powerpoint translate in english in the footer.

aJmooL is the non-official resurrection of Joomla 1.5 that fix the issue with PHP 5.4 but also security fixes.
We created aJmooL because we create the "Legacy" extension that give the possibility to make several Joomla version working together.

This legacy extension allows J1.5 working with J2.5 and J3.x
You can also use the legacy extension to make J2.5 working with J3.x
In this latest case, some fixes are required in J2.5 and Pull Request were created when we were at the J and Beyond 2014

So yes with the legacy extension it is possible different joomla version working together and it is possible to extension an exiting website runing under J2.5 with other functionalities that would work with J3.3.
Working with multiple version of Joomla may also require JMS when several menu are required for a give Joomla version.

We are in the packaging and final testing of the aJmooL and the legacy extension that will be release very soon.