Check to make SURE that only one side is grounded. Check to make sure that the place whare your grounding the ONE side is really a ground. Use your meter to check that your on a ground. I cant say this srongly enough, my wireing was correct, but I did not have the shield ground properly and as soon as I connected my shiel to ground the problem was solved.
You cant truely test the KS without an osiliscope in a running car.
I would make sure the wireing is correct. Test from the pin on the ECU plug to the KS end for continuity. Test from the pin on the ECU plug to the shield to make sure there is NO continuity. Test the shield to battery ground to make sure there is continuity. If the above test check 100% then it is probably a bad KS.
I am not sure if this next part will work, but it is what I would try because I dont have a spare KS.
Connect both ECU KS wires to the front KS, if the problem is gone then you know the back one is bad. If you still have the problem connect both ECU KS wires to the rear KS. If the problem is gone then you know the front one is bad. again this may not be a good test just what I would do. If this doesnt work then you may want to buy 2 replacement KS from a good source on the forums that are know working.
The last thing it could be is the ECU itself, that is very doubtful that the ECU is bad, but it could be.
Here is a link to a guy that used an o-scope on his toyoty 4x4 to test the KS.
http://www.cybertrails.com/~bestinthewest/autotips/995Toy88Knock.html
Good luck-
Steve