Second try: How can one load a large steel road bike for a short tour (in this case, four days) in such a way that the bagged bike and all its bags and other attachments may be carried, without considerable pain, through a large station and within trains, by a single human whose strength and number of arms are unexceptional?
If the cyclocross method of carrying a bike isn't an option given the bike bag, then I think you are down to weight training for this, unless something like this can be made to work
Though I wasn't fishing for tips on the bike itself, yours interest me. I have a "FibreFlare" (or similar) on another bike. I don't think they're available these days. I do have an additional, rechargeable light that I ought to attach -- it weighs little.
As it stands, the rear light on your bike is out of reach, so you either have to set it on before you leave (there are many people who recommend always having a flashing light on the rear of the bike), but if you want to put another light on for extra visibility, e.g. when entering a tunnel, then you are limited. With my fibre flare, I can just reach down and turn it on when riding. Fibre flares are still available: maybe they just pissed off the main retailers, but you can buy them direct.
The wheels are new and I'm not going to change them; but if a rim is damaged it's good to know what to replace it with. And the rims are Araya AR-713 (selected with 700x25 in mind). My understanding of rims is, er, limited; but here's part of a screenshot from Araya's website:
From the pic, the maximum width of the rim is 20.8, so a 28mm tyre is 135% of the rim width. Josh Poertner stated a rule of thumb (obviously dependent on the rim/tyre) that the rim should be 105% of the tyre width, so for a tyre of 28mm you should be looking for a rim width of 29.4 (maybe more depending on the actual width of the tyre once mounted). So there is a clear aero penalty, how much and how significant that is, I can't comment, but it certainly is costing you time/wasting effort. I've never retired a rim due to damage on the rim, so it is really your call as to whether or not the expense of a new wheel is justified. Also, I don't actually know what is a good rim for that size.
I think that when I pedal my knees normally keep at least averagely close together, and when I first attached the frame bag it tickled my thighs. But I very soon got used to this and/or adapted to it. I very rarely stand out of the saddle, figuring that this just tires me out quicker. (It's not a race: if I'm desperate because I find myself in far too high a gear, I've no qualms about getting off and walking a little.)
Here, I would say, that if you adapted to it by changing your stance, then always bear in mind that a change in pedalling style could lead to injury down the line. That's what I would be concerned about. As for standing, I do it for a few reasons - on steep gradients it reduces pressure on the knees, it's a rest for the undercarriage, standing allows full blood flow to the undercarriage to be restored for a short time, changes muscle usage.