1) Ditto on all Tom's comments (he's almost never wrong but don't tell him!;-) )
2) Congrats on fixing the messed up suspension - not a fan of the lowering links....the Gen1's springrate and damping is set up for a (largely mythical) 160lb rider....lowering links make that disparity much worse due to the increased leverage on the shock as Tom said.
3) unfortunately I'm building a house and my bikes are still in storage, but I can tell you that my two identical KLR's that were built 6 months apart vary in their sidestand lean angle....I think it's probably due to one of them having the stand mount bent in a bit. If you want a bit more lean angle, you may be able to bend the mount angle with a large crescent wrench but be careful not to get it too close to the swingarm or you'll gouge it when the suspension cycles....The spring pulls the Gen1 stand out (safer than the Gen2 stand set up) so play between the mount and the sidestand prongs can increase lean angle too - if that's the case, put it in a vice and squash the stand prongs until they are correct.
4) Yeah, nice bike! :-)