I took the catch can out and hosed it down, so I think I cleaned it pretty well. What do you recommend I should do? Am I not supposed to take out the catch can because of the air filter? 

You should probably take it apart hoses and all and give it a good spray and soak in degreaser to remove all the oil based products. then give it a good clean with fresh water allow it to dry and put it all back together and see how it performs after that. If you have a lot of blow by it might have to be a regular maintenance thing. Remember that vapourised oil is super sticky when it returns to a liquid it clings to everything. So clean the whole system.

Do all of the above ,then give it a compression test .

This will tell you if your engine is needing rings ,thus causing all this blow by.

To put it back to stock means welding/drilling a barb into the base of the air filter and putting the front hose onto that, not a big job at all. Then screwing a barb into the inlet manifold somewhere (there should be a hole already for it, with some threaded plug in it) that the rear hose goes onto with a PCV valve fitted in it.

So at idle the high inlet vac closes the PCV valve off and the little blowby you have goes out the front hose to the air cleaner and gets burnt. Then when you are accelerating & there is lower inlet vac the PCV valve opens and the inlet vacuum sucks the greater blowby into the rear hose and burns it.

The idea is that when the motor is not working you don't get much blowby so you don't need to vacuum out the block. When the motor is working hard you get lots of blowby and the inlet vacuum sucks it all out and burns it. At that stage fresh air is admitted in through the front hose via the air filter.

As Rob says, get a compression test done and see what it reads. 130psi is just OK, 150 is fine and anything higher is great. You will also work out how much oil it is burning after a while..  half a litre per 1000km or whatever.