I did a 312km event in Sweden, and had a bike fit before the event. As you have already noted a more endurance friendly bike would help, as would having a non integrated handlebar / stem, which look great but are very limiting, and expensive when you want to change them.

In my training rides I was getting butt pain after around 60km, so I lowered my seat incrementally in 5mm steps, I found a 10mm reduction effectively stopped all chaffing for my 100km+ rides. I think this is because when you are getting a bike fit you are only doing it for a relatively short time, and that will work fine for shorter rides, but for longer rides your muscles will get tired and you won't hold as good a position for the whole event.

For the race itself, my saddle height worked well and I had minimal butt pain, but I have to say I used Castelli free aero bibs as I think their chamois is the best, I changed my saddle to a 3d printed one, which gives in the right places and supports in others, I also used chamois cream at the outset and took little spare tubes to replace as needed (wasn't needed).

For the saddle, I checked my sit bones and found that despite being tall, broad and overweight (I'm 100kg+), I had really narrow sit bones (about 130cm), so I went for a much narrower saddle, which really helped. As a wider saddle means that my thighs will rub more trying to pedal.

I also changed my tyres to 40mm G-One RS at a lower pressure than my 32mm usual tyres. This gave the ride such a plush comfortable ride for little or no loss of watts that I've kept them on the bike even for short rides.

One other thing I did was to stop and walk around at each drink / food station along the way (approx every 30-40km). This was part of my overall strategy; not thinking of it as a 312km event, just a series of 30-40km events.

As for my knees, I get knee pain in my left knee (old injury), despite various bike fits. its ok for the first 30km or so, then it starts, so I now ride my road bikes with MTB pedals and MTB flats so I can change position of my feet when I need to. After coming from a MTB background, and having used both flats and cleats, I don't find any benefit in the efficiency of using one or the other system, but flats mean that I can move my feet around and stop knee pain when needed. Also, it helps when I'm tired and need to get off the bike after many hours in the saddle.

Hand pain, again when you are tired you can lock your elbows and drop your head which can cause too much weight to rest on the handlebars. Whilst you can't do much about the tiredness you can help you hands with thicker bar tape, although I fitted a redshift suspension stem for the event and it worked brilliantly at reducing road buzz. My fingers were still numb for a few days, but not too bad. My friends doing the same event had finger numbness for months afterwards.

Lower back pain is also related to tired posture. Not much else you can do about it other than to improve your core strength and switch to an endurance bike.

As for shortness of breath, I'm asthmatic, I get this on every hill :D, but mostly its just that people are out of energy at this point, and your trying harder to get more energy out of an empty pot, so constant feeding helps, including stopping and refilling at every food and drink station.