Hey dude,
We recently took down a 15-unit apartment complex with the same issues... popcorn ceilings and wood panel walls. I suggest getting rid of the popcorn without thinking twice, the stuff makes a mess and no one likes it anymore. The wood panel is a much more difficult question primarily because:
1. Ripping out the wood paneling/disposing it is costly and drywall/mudding and taping for an entire complex is going to hit your rehab budget hard
2. I don't have intimate knowledge of your market and what type of finishes you can get away with
We elected to rip out the wood paneling and install drywall only because we are doing a complete re-wire as well. That said, the comps in our area, along with the cost savings of keeping the wood paneling, justified our original plan to keep and paint the wood paneling.
My best advice - check out the comps and be honest with yourself. If you can still hit the $1,045/unit number with the wood panel, it's a no brainer to paint over it for now and possibly update each unit individually as tenants move out down the road when the comps justify it