For current upgrades, HocusLocus has the right idea with purchasing a speaker-level to line out converter. This lets you connect directly to the backbox speaker leads and avoid messing with the Spike2 board. Get one of those, connect the inputs to the backbox speaker leads, and run the line out to your amp. Nowadays, the amplifier/equalizers I used aren't available, but there are plenty of small 2.1 amps to use, like this Lepai model:
https://www.parts-express.com/Lepai-LP-168HA-2.1-2x40W-Amplifier-1x68W-Sub-Output-310-308
You would connect the Lepai directly to replacement backbox speakers and a new cabinet subwoofer. Here are all of Parts Express's 4" speakers:
https://www.parts-express.com/car-audio/car-speakers-subwoofers/dash-door-deck-car-speakers/speakersize/4.0
Lately I've been getting the Visaton FX-10s. These have the tweeter flush with the surround ring, so you can install them behind the Stern grilles no problem. They sound good and are only $20ea.
https://www.parts-express.com/Visaton-FX10-4-Coaxial-Speaker-292-674
For the cabinet sub, you don't really need to spend a lot. $20-$30 subs work fine. Here are all of Parts Express' 8" subs:
https://www.parts-express.com/car-audio/car-speakers-subwoofers/car-subwoofer-speakers/nominaldiameter/8
This Pyle is only $20 and would be fine in a pinball application. You can always spend more but I have yet to blow a sub in a pinball.
https://www.parts-express.com/Pyle-PLPW8D-Power-8-800-Watt-DVC-Subwoofer-267-7452
I recommend removing the plastic grille to keep the sub cone from buzzing it. Also, if the game is a Spike 2, go into the settings and set for 4 ohm and remove any equalizer or filter settings. Use the bass/treble/sub controls on the amp to adjust the sound... I wouldn't trust the digital adjustments the game makes.