86 runner
rear window functioned normally.
took off top, replaced,
now, from the driver seat-
up and down operates normally until it reaches half way
then only up works
Rear key operation is normal through out

Break out a volt meter and check signals at the relay box when it works and when it does not:
- http://www.4crawler.com/4x4/CheapTricks/RearWindow.shtml

Any differences will lead you to the problem cause.

I knew it, post a question and its solved it self.
I didnt do anything but I have full fuctionality back. weird.
Its been half functional for 3 weeks. And the drive I take after posting
HEALED
thanks though

Probably just dirty contacts in the switch from not being used in a while. Operate them a number of times and the dirt might have been worn off.

Well, took the top off during the heat wave and when I put it back on, I have that functionality problem again but at a different window height. I can roll the rear window up to about two inches before full up position, and the button op front wont work to bring it back down, Untill I use the rear key switch to bring it down a few inches, but will complete the upward motion. Again the rear key function works throughout the travel. I was super careful about lining up the top, giving it a few good settling shakes,
I just dont get it,
Im going to take your link advice and troubleshoot it, but im curious what limiter is creating the mis function.

You might try the modification below that makes the interior switch work like the rear key switch:
http://www.4crawler.com/4x4/CheapTricks/RearWindow.shtml#Relay

That is it works with the key off and also bypasses some of the interlock switches.

is the motor still spinning or does it just stop? I had that problem when my gear on my motor wore out.

OH Yeah!! Thats what I did to my other toys!
So I pulled the control box, Made a jumper "staple" from paper clip to insert into the top of the connector bridging the 4/11 5/12 areas. Wala, it works, but only works Fully when the truck is off.
If the truck is on the window rolls up and down fine untill it hits the top 2-3 inches, then the switch goes dead for down only. turn the truck off and it works fine.
An improvement for sure but still a wee PITA

Well then it looks like you need to do some troubleshooting to find out what parts of the circuit are active with the power off and on and narrow down your search to the differences in the above two cases. Probably only one or two switches in play, so should not be too hard to find out which is acting up.

For example, put the window into the position where is stops and check the voltages on the relay module connector. Do this with the power off and on and see which are different.

Make sure your tailgate is fully latched as there is a limit switch in the latch. I think it needs two 'clicks' on both sides.

Mine had an issue where the left side was half-latched but the switch made contact until the window was almost up then it pushed the tailgate open just enough to break the contact.