Some of this is just the nature of the bike. When I first started riding my 426 a few years ago I had the same complaints Running a different sprocket set up will help a bit, but its not going to make a huge difference for what your trying to accomplish. I was also riding an XR100 before and rode an XR250 for a bit too. Most of it comes down to changing your riding style. There really isn't a "one fix all" for what your trying to accomplish. Don't let it discourage you though, I love my bike for woods riding, but it kicked my ass for awhile.
Here is what I did to make things a little easier-
kit (in my opinion its essential if you trail ride so you can ride at different altitudes/temperatures)
Sprocket set up to your liking
CLUTCH (amazing difference)
I just installed a Z Start Pro Rekluse
clutch on my bike about 5 rides ago and it was by far the best thing I have done to this bike or any of my other bikes for woods riding. It eliminates a vast majority of your difficulties with this bike for trail/woods style riding . It does not, however, help with downhill engine braking
that much. You'll find that if you want to get any compression going down hill in first gear your going to have to be moving pretty fast. Oh and if you are thinking about getting a rekluse clutch don't bother touching your stock flywheel. With the Rekulse you won't need to worry about it. The only con is that it is a bit expensive. If you install it yourself (its easy if you follow the directions) your looking at about $640 bucks.