The foam plug in the mid/woofer is there to prevent debris from getting into the motor structure. It may have a small effect on damping too, but it's so porous that it would be a minor reduction in Q.
The dust caps can be lightly coated with latex if you wish, Make sure it's an even coat. I'd probably do that myself as the woofer is already vented at the back, and keeping it air tight in front should slightly improve the bass response.
I obtained the schematic for this exact model, and there is an error. Since yours are apart, you can see what is incorrect in the official schematic. Take a look at the wires colors and lengths going to the tweeter. In the schematic, it shows the tweeter wired in the same polarity as the mid, and woofer.
However, see the wires! They are cut so that the tweeter is wired in opposite polarity from the mid!
In fact, if you try and reverse those leads, you'd need to lengthen one wire and cut the other. While this seems intuitively correct to keep "first order......" crossover topology, it actually will result in the tweeter and mid being out of phase at the crossover frequency. Try it if you wish - there is a very audible suckout in the upper mid range if you wire it, per the crossover schematic. Someone just made a small typo..
The tweeter circuit was changed on this model from the previous version. In the S.80, the capacitor going to the tweeter leg was 6.8 uf. In the S.80.2, it was changed to 3.3 uf., but the tweeters themselves are the same, or nearly so. The designer took into account the actual response curves of the mid range(changed in the two models)and made a wise choice in permitting an out of phase electrical filter, to put the acoustic sums "in phase". This also put lower demands on the tweeter.
I eventually swapped mine out to a later version of the Vifa tweeter; this one with a good sized cavity behind the dome to lower fs. I also ended up slightly padding it down with a 1.2 ohm resistor before the cap/resistor shunt that feeds the tweeter leg. I felt this necessary because the new tweeter was slightly more efficient then then the original.
This mod took away some of the sibilance the S-80.2 had that was bothering me, and smoothed the mid range through high range transition. It's actually a very fine sounding speaker with a little bsc of around 4 db(in my room), per Murphy calculations. Google for that if unfamiliar. Then, actively crossover to a good sub woofer system, and you'll be impressed!
btw - I hope you bought the exact replacement foam for those woofers? Nothing generic will fit right, or at least nothing I've come across did.
best wishes, and happy holidays!