Questions about Knee Issues.

go see a reputable PT asap

Like the previous poster said -- make sure the knee isn't damaged. Rest, ice, etc. See a doc if doesn't improve.

As for moving forward:

I'm not sure which SPD system you have, but the models I've known/used in the past have some kind of float built in (up to 8 degrees in some cases).

Have you checked to see if your SPD cleat setup is similar to your Speedplay setup in terms of fore/aft and foot angle? Perhaps you have the SPD setup in a way that is compromising your foot position and/or pedal stroke. Slap your speedplays on and spin for a bit. See where your foot is ending up in terms of heel in/out, etc. Do the same w/ the SPD and see if they're comparable. If not, adjust.

Is your hybrid fit setup significantly different than your roadie? Seat height/location significantly higher/lower on hybrid? That could be one issue leading to knee discomfort.

Where you ready for 100 miles physically? Not a knock, just curious if you've worked up to that distance or just decided to gut it out. Fatigue is a huge contributor to bad/sloppy cycling form, which can lead to injuries.

Note that there are a multitude of variables that can lead to knee pain while biking. Make small adjustments, and try not to change too many things all at once (hard to nail down which adjustments helped/hurt).

I use both Speedplay and Look, and I've attempted to mirror my cleat positioning between the two systems w/ no issues, so you don't have to necessarily be locked in to one system for all bikes. Any pedal system not set up correctly will have adverse effects. Speedplays are nice if you're not sure what float or angle to use, as your body will naturally gravitate to its ideal position.

Hope you have a speedy recovery!