to do this you'll have to set up macros and keymaps that are focus based i.e. not FTL
No you dont...

I need the ability for my tanks to NOT assist the current window when asked, and I can't find any "except" kind of script in ISboxer that will exclude certain windows, characters or classes from the FTL thing.. what am I missing?
What you're missing is that you're asking how to modify the "FTL Assist Me" mapping under Control, which sends assist to "all other". If you want to change who it goes to, you can use Action Target Groups. You can dynamically control who assists you by adding or removing them from the ATG.

Make an Action Target Group called "assisters" for example. Add every single Character to it -- you can do this quickly by selecting the ATG in the top pane, then right click on "Characters" in the bottom left and there's an option to add all. Then change the action in FTL Assist Me to send to Group (others in) assisters, aka "other assisters". Then make a toggle or something with a Target Group Action that can remove your tanks. Put them in another ATG called tanks or something, and your Target Group Actions can tell all tanks to join/leave the assisters group.

But definitely don't switch to focus just for this