Firstly, sorry for the long answer and I know, it too detailed and also, many have there own proven methods....but I just found myself with more time on my hands today than I thought
Nice historical example that has clearly 'been there, done that' and I love that about such WW2 pieces (if they could only talk). Apart from professional polishing of blade (and thats probably not worth it), please don't 'upgrade' the remainder as its very nice as is.
On the seppa, yes it looks like it is missing one but, as you say, it could simply be the lack of mekugi. So fix that problem first and see how it all fits and if you still need to tighten things up a little then you could consider a small seppa (original please/no repro's)....or even a compressed leather seppa. PM me if you would like any tips on making a 'respectful of age' mekugi or leather seppa.
On the matter of leather preservation...everyone has their own favourites. But for what its worth, I use ' Renapur ' Leather Balsam. I have used Dubbin and similar products and they are very good but Renapur is used by some large museums for their leather conservation and I just wanted something from 'the top shelf'.
Some find it too sticky/gluggy and it is, BUT is absorbed over a period of 48 hours or so. Firstly, only use it on the treated side (outside) not the suede leather sides. Use disposable gloves and apply it generously using a piece (cube) of sponge. Slowly and gently. Use a cotton bud for any really small areas that you need to get to but again, slowly and softly. Leave the saya in a moderately warm area for at least 2-3 days and you will see that it has been absorbed. Then you can very lightly buff the outside of the cover to bring up the shine that was there before you started on the smooth/treated sections of leather. When I say 'lightly buff', I mean it. I roll a micro fibre towel (approx. 30cm x 30cm) into something the size of hotdog and then loosely wrap a piece of well worn flannel over that and then very lightly but quickly dust (i.e. like a fast light rub over the whole saya gradually increasing pressure (but only moderately) until you start to see the shine come out. If you feel any resistance when you start then STOP and lighten up. You will reach a stage where there is no resistance on the shined leather but the scuffed leather will always resist this buffing so just leave that alone. You wont shine the scuffed leather and this, and other similar products, will slightly darken the whole saya but that's just restoring to a rich more original tone.
It then up to you if you want to apply shoe polish to certain areas but I don't see the need.
Now one question for you Tony, the saya drag that is protruding from the leather combat cover looks like a worn drag from a Type 95 but yours is clearly a Type 98..bit confused about the look of that. No question about it being genuine, its just that, from the picture, I haven't seen a Type 98 drag like that before. Other may have an answer for this (probably just my inexperience) but if you don't get a response to this query, could you post a picture of the saya throat and a better one of the drag.
All the best.