Yeah I'm not the most popular at the moment, I am only just hanging on to a 3 vote majority, luckly no other nation has anything more than a single vote.
I didnt know the annexing thing stacked so hard and took so long to cool down, I think I'm at like -67 (+1.7 yearly) which is going to take forever, and I have two more annexations that are completing shortly.
For vassalizing minor electors, if they are still small I'd do that. In my last Austria play through, this was my first order of business. You can just use the revoke electorate CB that you have on them, quickly occupy them and be done with it. I grabbed Cologne, Trier, Mainz and the Palatinate (this last one since is a kingdom and you can potentially inherit their vote with kingdom). While they are all minnows, they do help out in wars. If you keep a small 2-3 size stack of mercs to siege, the small vassals will typically link up with them while your big stack does the battles. You have Bohemia in PU now, but unfortunately you don't get their electoral spot upon integrating them - only inheriting.
For the religious unity, I only used it when they say yes. Make sure to check out their reasons for no as sometimes they are borderline and a few months of improving relations will switch them from no to yes.
Finally for the minus relations that you are waiting to get rid of, you just need to unlock the Austrian idea which buffs your better relations over time!