* L1 is sitting on analog ground and shouldn't be there, it will make sound performance worse due to ground bounce related problems aswell as not letting any HF noise return. It is best shorted out as on the later card.
* L2 is WB 5V power filter inductor, it makes WB card power slightly less noisy and prevents noise coming back to the host card to an extent.
* L3 is gameport power filter inductor, is there primarly for EMI reasons.
* C56 and 53 don't make any difference to operation, they should be EMI filters for MIDI I/O signals on gameport. They should be 1000pF at most.
* I'm not sure what CA1 is, I'm not at home to look at my cards to see exactly what it is.
* RA1 is part of the reset handling circuit on one of the cards.

For the lowpass fix you need to get a handful of capacitors and find one that suits you best (or use whatever the guide suggests). 1000pF, 1500pF, 2200pF, 3300pF, 4700pF, 5600pF NP0/C0G ceramics in 0805 size are things to get.

The connector near microphone is carrying microphone aswell as YMF71x mono in signal IIRC. It could be used with PC-speaker but it requires a special cable or modification to the card as it is still providing a regular line input and not something that can take PC speaker 5Vpp signal.

Great! I can take L1 from the other card and place it on L3 to the other. Both cards get better and no extra components needed.

I'll order different capacitors for the lowpass mod just in case then.

So the connector near mic input contains two mono inputs? I suppose it is not possible to configure them as another stereo line in, other to the left and other to the right only?

Just be sure to take care of the link in the inductor path in part footprint center location, cut on one that gets the inductor, bridge on other card that gives it up.

Stereo input is not possible on that connector, you only get two mono signals there that you cannot pan.

I finally did the fixes. I removed the L1 from the other card and it was already shorted under the inductor. I moved that inductor to L3 on the other card (and cut the trace before soldering it). I did the wavetable reverse stereo fixes and changed the lowpass capacitors to 6.8nF SMD capacitors as suggested by the guide. Then I added the missing C53 and C56 to the other card. I used 1 nF SMD capacitors for that. Last I recapped both cards since this was a good time to do so while doing the other mods.

Now the cards look like this. I tested both cards with jumpers set to line out and speaker out and with gamepad. I also tested X2GS with both cards and everything works (but CT11 and CT5 capacitors are now so tall that they touch the X2GS PCB). These cards are now better than new and really good cards. But not perfect, nothing is.