You can flush out the tranny with a 50/50 mix of paint thinner and engine oil, just install the mix and let the bike idle to warm it up then drain it ,then install some regular tranny oil and ride it for awhile to warm it up again then drain it again,this should get any water out if it is just from condensation.Refill it once more and if the oil turns milky again then the pump seal is most likely the problem,You might be able to get a shop to pressure test the cooling system for you.This was a common problem on the 89-90 kdx and for 91 they installed a second thin back up seal,the second seal will fit in the 89-90 so you can upgrade,check the water pump shaft for grooves and replace the bearings x 2(they can be bought at a bearing shop,part # 608-C3 open no seals)at the same time,they are only a couple of bucks each.