Just finished a GEn1 rear suspension service today. Dog bone and swing arm bearings were near perfect but the through bolts were seized for the swing arm and the big through bolt for the dog bone. Not unusual at all but with some 12 pound hammer and brass drift, they came out. Not as bad as some which required drilling.
Some suggestions:
These bolts usually seize to the bearing sleeves but can also seize into the case or structure. Turn the nut to just flush with the end and use a big brass drift and hammer in the 10 pound+ range as a lighter hammer typically just rivets things over. After a try at driving, check to see if the bolt as moved at all. If has moved, squirt in some penetrating oil or ATF and drive it back. After knocking it in and out a few times, try turning the bolt. If it turns easily, it is seized into the beating sleeve(s). If it does not turn, it is seized into the surrounding structure- particularly common for the big dog bone bolt.
If it does not turn, or turns reluctantly, and is through aluminum (such as the big dog bone bolt) don't rotate the bolt more than one flat in order to loosen., just turn back and forth. Turn, then drift back and forth, then repeat. Don't become too ambitious as over stressing the aluminum engine case will be bad news.
Forcing the bolt to turn within a seized engine case hole can displace material and further jam the bolt. The effects can be concentrated into a small area and result in breaking out a portion of the engine case structure. Small arcs can help to loosen but not too much rotation.
Usually best with these to lubricate and knock back and forth. This is essential with seized bearing sleeves.
The KLR through bolts can withstand some quite heavy hammering, IME, unlike some other bikes.
As others have said, important to limit force to a reasonable degree and to coat with a good waterproof chassis grease.
Good luck with it. Welcome to bring it by if that helps.