This video series is very useful and super inclusive:
A summary (work in progress, he says a ton more than this):
Make sure the engine is cold when you first see it.
If a bike has been sitting, that's the worst thing you can do for it.
Check the tires.
Rust in the tank sucks.
Is there an inline fuel filter?
Specific to the XJ series:
The fusebox is a weak spot; it's located underneath the seat. Check its condition, and check if it has been replaced that it was done well.
You DO NOT want pods on the bike, as a rule of thumb. Rarely does one get the bike running well after switching the airbox out for pods. You can find and buy a used airbox if the bike in question doesn't have one.
If you see short pipes, there's little chance that proper modifications were made to the jetting to accomodate the increased airflow.
Look at the carb-to-engine boots (carb joints/manifold/manifold boots). These often crack and let extra air in, causing severe running problems. These are $50 a piece, so keep it in mind. (There is a homebrew option to "restore" these that involves RTV and bicycle tube.)