Please reconsider using filter , widen it, do a big box and put a wider filter so you can span the filter cleaning or changing period.
Other good way is to route freshair from a clean air place, it can be done from te roof or a near window.
If route is a long way , put a blade fan on the intake.
Other way could be to change the heat exchanger by a water cooled one, maybe there is a water cooling tower system piping.
Other is to split the HVAC equipment , and put the condenser on the roof , a fan shall be added.
Other is to change the HVAC by a split system.
I had handled about 260 units on a manufacturing plant.
It had filters , a nowoven fibers 25 mm thick.
What is manufacture at such plant???
Hope this helps tip , help you.
Pardal