Sorry, I have forgotten much of that technical data. I used to be really interested in both those bikes.
How about some subjective data instead? The Honda XR650L makes very low HP number in stock form for a number of reasons. Mainly that the engine does not like to rev. I believe the peak RWHP was about 32HP. Mods can easily bring that number up to above 40. The Honda has a wide variety of performance and aftermarket parts available. In stock form the Honda tops out at about 89-93MPH. Be prepaired to spend some money to uncork the bike. Even the camshaft is very mild.
The Kawasaki KLX 650(not KLR) is in a higher state of tune right from the factory. Simply adding a non restrictive exhaust, re-jetting and unclogging the airbox will result in about 45RWHP. Stock top speed is around 103MPH. The aftermarket does not offer much for this bike.
As far as which bike has fewer emissions, I suspect that in stock form they both are very close. Both are 650cc single, non catalized, non EGR'd engines with fairly lean jetting. The fuel burned will probably be similar and therefore so will the emissions. Having owned both, I believe the fuel economy for each was about 55MPG on the highway at reasonable speeds. Expect about 25MPG slogging through the mud. Trail riding is somwhere in between.
I like em both.
Chris