So, Teleport Through Time, retroactively cast an Epic spell that counters all Disjunction effects targeting the party. Done.

Maybe price the Bracers of Shared Contingency as Arms of the Naga & a feat (aberration heritage for longer arms), and only allow them to function a) on spells that could work at range touch (like Teleport); b) only within a limited range.

Honestly, the best answer (IMO) is just to let everybody have their own Contingency. No need for custom items.

Also, it sounds like you've heavily house-ruled the beautiful array of colors in 3e down to black & white, and are now feeling the pain of doing so. Yes, if there are a very limited number of viable tactics, then it becomes very easy to defend against them. Or, in common parlance, limiting offensive options has given a stealth buff to defense. You've made defense king as a logical consequence of your world-building. Now, you've got several options, a few of which are:

You can let the players' plan work, like you think it should. This might make your players feel smart & their PCs feel awesome, or it might make your BBEG feel like a chump.

You can change the rules. This might make the final fight more enjoyable, or it might make you look like a chump.

You can try to let the PCs plan work, and make the final fight with the BBEG seem a fun challenge. Depending on how much you've butchered the rest of the rules, the Playground may or may not be able to help you with that without getting an associate's in "your world". This path is hard work, and could give you every success... or every failure.

Also, out of curiosity, how was the party supposed to have a chance against (Disjunction and) high-DC AoE SoD without resorting to bring immune to the BBEG's schtick?