Hi and welcome to YT
.
The GI issues could likely be from the deworming product as sometimes these cause upset...so that would be my first suspect.
As far as the shots, I never ever get rabies in conjunction with *any* other shots on the same day. So, his system could've been overwhelmed in general with all those shots at once.
One thing you could try is going to PetCo and picking up some Benebac to help properly populate his GI flora, it may help a little.
Have you smelled his ears...do they smell funny? If so, he may just have a mild ear infection.
I hope your precious one feels better soon!