I've had my passing offenses leaning very heavily on medium distance passing. I am not really sure how great short passing is tbh, what are the best routes to use in short passing?

It depends on your players. What I find works best is experiment with a play and see what the average distance gained after 5-10 or 10-20 plays is. If the average gained is above say 5-7 yards, then it's a keeper. If not, move on.

Yeah I have a few teams where I'm struggling to hit a 50% completion percentage and would like to make those teams a bit more efficient.

Yeah, that's the unfortunate thing about scouting your own plays. You can't tell the completion percentage. For instance, a play that goes for 4.5 yards with a completion percentage of 70% is more valuable than one that goes for 7 yards with a completion percentage of 40%, but we have to work with what we have.

Not to mention those averages could very well be thrown off by hitting that play for a big gain once or twice.