With 5000 miles with nothing more than an overgrown dirt bike under you, there are some modifications to add a bit more comfort. Your hands, feet, rump are in constant contact with the bike, so I added some bling to take the edge off.
Having hand, wrist, and elbow issues, this is a significant concern for me. Two things I have added to take the edge off the long hours are best dual sport bikes dead ends and A’ME clamp-on heated grips. I know from riding my thumpers and working with grinders at work that hours of heavy vibration in your hands can make for a day of numb hands and is extremely fatiguing. To reduce this; dead-end bar inserts by best dual sport bikes add weight to the end of the bars to minimize the constant vibrations. It does take the bite out of my bars, it is not a turning the bike into a big adventure bike, but it helps. 
Then there are cold hands, I don’t care what gloves you wear with vibrating bars and clamped hands blood does not flow that great, so an external heat source is a key to keeping those digits from going numb and aching. The A’ME heated grips answer this problem with a minimal power draw of 10 watts, I am still in a safe range of the 500’s 90 watts. The downfall of the A’ME grips are the separate controllers for each grip can be a pain. (the new version have a single controller)
What you sit on for 8 hours can ruin a great day. The design of the stock KTM 500 seat is for movement around the bike and not for sitting. Sort of like the old plastic BMX seats from the ’80s, and about as comfortable. I have read about people using all kinds of different methods to make 5000 miles on a dirt bike saddle more comfortable, from beads to sheepskins. In the end, my seat is designed to ride fast for a short period. So a custom saddle was the only answer to making a KTM 500 kinda comfortable. I looked at many custom 
saddle companies, and I found Fisher Saddlebags, a small company in Idaho. They make beautiful saddles, especially for this kind of ride. There is a detailed measurement form and lots of questions after they receive the stock saddle you need to answer, but I think the final product will make me very happy.
Then last but not least are the most significant connection to the bike, your feet. Stock pegs are small and don’t get in your way when paddling and are easy to move around on. But with hours on the pegs day after day, a bit of width and a flat platform take the edge off. Pivot Pegz much wider than the stock pegs on the 500 and the pivoting action takes the stress off your ankles when wearing off-road boots. The width of these pegs supports your feet much better than stock. CJ Designs offers extender at 1 and 1 5/8 inch, but I find the extensions become a hindrance on tall bikes when paddling.
