Though it's easy to drop $1,000+ into mods for Theatre of Magic and Twilight zone, PM isn't a mod-heavy game.
In fact, I think I've seen a single mod (enhancement) for PM. It was a female magician bust that someone found online and mounted atop a playfield plastic.
If you change rubbers, given that the flippers are strong and the game is fast, I highly recommend NOT to install Superband post sleeves.
LEDs
Can't do LEDs.... not yet.... not until Herg figures it out and offers an LED OCD product (this is work in process - thread here https://pinside.com/pinball/forum/topic/leds-in-capcom-games).
Wireforms
When I take my game down for shopping, I'll most likely pull the wireforms out and send them off to Chestnut for some high-polish brass plating (they'll look like they were gold-plated). Not really a mod, but a nice touch that will make the game pop!
Protective Upgrades
Pinbits has some playfield plastic protectors for PM, but not a complete set. IN fact, I don't even think it is on their site. I've been trying to get Bryan Hansen, the game's original designer, to forward CAD files of the plastics so pinbits can make a 100% set. Otherwise, I'll take my plastics off when I shop the game and scan them to achieve the goal. Either way, you'll eventually be able to get a full set from Pinbits and that is important since you can't find most replacement plastics on the market. www.pinbits.com
Mantis makes a replacement lift plate for the 5-target bank. If you look at yours, it's Aluminum and probably pretty nearly worn through from making contact with the two stainless leveling screws beneath it. I had Kerry make me one out of Stainless, and that is what I'd recommend you purchase from him. http://www.mantisamusements.com/pmdrop5.htm
Finally, my buddy Robert just shipped off a spare NOS playfield to Cliff so he can template some protectors for the skill shot, shooter eject, and most importantly the genie bottle hole under the trunk on the left side. Stay tuned, as these should be coming soon.
Hope this helps
-Brian