Okay, on the basis that it seemed like the best[1] way of doing this, I've invested in a number of individual patches as mentioned up thread.
Today, I applied them:
I patched the main holes (thumbnail-sized, in the PS490 side section) using a large piece of PD620 on both the inside and outside. The inside patch overlaps the join between the pannier's two materials.
First I cleaned the area thoroughly with citrus-based degreaser stuff, to remove the gaffer tape residue from the temporary patch. Then wiped it down with methanol to remove the degreaser. After cutting patches to size (with nice rounded corners to avoid snagging), I applied the glue as per the E163 kit instructions: Copious amounts to both surfaces, and allow to dry for two minutes (which takes it to the tacky side of completely dry) before placing the patch. Then apply pressure for a couple of hours (in this case by stacking dictionaries on top of it) while it dries. As there was a large amount of missing material, I cunningly placed a piece of card inside the pannier while applying the outer patch, so it wouldn't glue to the opposite side.
This appears to have been entirely successful - the patches have bonded securely to the material, and unless something manages to snag an edge, I expect it to be as durable as the rest of the pannier. Looks pretty awful though, as it's an obvious patch of PVC on the nylon area.
For the less serious cut on the bottom of the pannier (a centimetre long clean slit in the PS490), I used a single patch of PD350 on the outside. This is the thinner PVC material used in the 'plus' version of the panniers, which is more flexible, and being less shiny, a marginally better cosmetic match for the PS490 nylon. Given the location, I reckoned a more flexible material would be worthwhile, as it tends to be where the material folds when the pannier is packed flat.
This also bonded well, though I managed to cock up the application of glue to the nylon surface, leaving a ~5mm strip down one edge of the patch that didn't stick. I have cleaned and re-applied glue to both surfaces (holding the edge of the patch back with fingernails for a couple of minutes while it dried), and I'll leave it under pressure overnight. Fingers crossed it will be okay in the morning.
Initial impressions are that the adhesive in the E163 kit does what it says on the tin (that is: a generic waterproof seam sealant/adhesive effective for PS490, PD350, PD620 and various other materials commonly used by Ortlieb). The patches supplied in the kit are small, transparent PVC material - if you're repairing a pannier with anything other than a small puncture, I'd strongly recommend a more substantial patch of matching material, but they're probably useful for tents, airbeds etc.
Obviously if you're patching PD620, I recommend a colour matched PD620 patch, but I reckon the PD350 is actually a better match for PS490 in terms of flexibility (and since Ortlieb make the newer panniers entirely from it, it should be fine for durability). Unfortunately, patching woven nylon with PVC is going to look fairly awful cosmetically whichever material you use. There's an argument in favour of the 'plus' versions of the panniers on this basis alone.
Don't skimp on the glue, and it's well worth sticking a second patch internally if the damage is non-trivial.
I'll take some photos and do a leak-test tomorrow. And see how it performs in use on the Scottish camping trip at the weekend.
[1] "If you're using adhesives," said Kim, "you're probably doing it wrong."