So I tried to test out the manual closing procedure while the batteries are disconnected, and pull that Orange Lever underneath the back seat. Well, I felt two clicks but top will not release. Also, when I removed the trim, I only can re-engage the motor that faces the front of the car. I don't see any other motor that I need to re-engage, weird.

Hmm, I've never taken that avenue, so I don't have anything to add here.

Hmm, not sure where the other motor is. I think it's attached to the 1/4 panel. Well, I'll find it soon enough, after the diff. fluid change, and the instrument cluster goes back, I'm testing out the top again. Just seems to have much more issues with this than my Trusty Jettai Knight!

That motor is on the left side behind a brace. It is hard to see, but it's there.

It sounds like you have the fully auto top and you pulled the release bar with the top up. You will need to lower the top. I have a semi-auto top so I am not positive, but I believe you should have a tool somewhere in the car that you use to unhook the top from the header. If anyone knows where it is, please chime in.

I have a couple of pdf filse that will help you with the reset procedure. Both show the locations of the motors in the trunk. But the files are too big to attach here (175k and 879k and there is a 150k limit per file). Post your email or PM it to me and I can send them to you.

-Matt

Being that your vehicle is a 99, I am assuming you have the fully automatic top. I will tell you that if the cables are not tight, the under seat release will not release both motors. There are 3 motors that work the automatic top. One is inside the plastic covering that that unlatches the top from the windshield. In order to get to it, take a small flat head screwdriver and remove the small square cover. You should have an allen wrench in your toolbox in the trunk that fits. It will take many turns to get the top unlatched. Make sure you get it back as far as you can so that it releases the tension on the back of the top. The other 2 motors are on the drivers side quarter panels in the trunk. One is mounted directly below the top on the left and the other is mounted to the side. Make sure both motors are disengaged. Once you move the front top as far back as it can go, motors disengaged, you should be able to raise the back of the top up. This should allow you to raise the clam shell/boot to store your top in. You must make sure your trunk is closed. Once you have done this, re-engage your motors and then use the initialization procedure.

No, the top is down right now. I want to get it back up using manual procedure since the instrument cluster is removed at this point.
It sounds like you have the fully auto top and you pulled the release bar with the top up. You will need to lower the top.

Thanks for explanation. What's interesting is that the top is down, and the storage compartment is closed. When I pull the lever, I feel two clicks, but, when I tool the cover off the LEFT side of the car, I see one motor is disengaged but the one on the LEFT quarter panel really has no connection to the emergency cable. Also, the car did not have the allen wrench in the tool kit. So I would either make one or buy one. When I pull on the emergency handle, the compartment lid should open right? It's funny that it does not. Now I 'm not sure if I have re-engaged all the motors..
Being that your vehicle is a 99, I am assuming you have the fully automatic top. I will tell you that if the cables are not tight, the under seat release will not release both motors. There are 3 motors that work the automatic top. One is inside the plastic covering that that unlatches the top from the windshield. In order to get to it, take a small flat head screwdriver and remove the small square cover. You should have an allen wrench in your toolbox in the trunk that fits. It will take many turns to get the top unlatched. Make sure you get it back as far as you can so that it releases the tension on the back of the top. The other 2 motors are on the drivers side quarter panels in the trunk. One is mounted directly below the top on the left and the other is mounted to the side. Make sure both motors are disengaged. Once you move the front top as far back as it can go, motors disengaged, you should be able to raise the back of the top up. This should allow you to raise the clam shell/boot to store your top in. You must make sure your trunk is closed. Once you have done this, re-engage your motors and then use the initialization procedure.

You might want to take a picture of the one on the left quarter panel, I am not sure what you mean about not being connected. To re-engage the motor thats on the left quarter panel, put your hand behind the motor and pull it toward you, it should lock in and re-engage. The convertible top is a pain the rear and can be temperamental, but its worth once you get it fixed.

Okay, I will take off the panel. BTW, it's flashing now. I guess one of the motor is not engaged.

BTW, I got the Instrument Cluster back in, it wasn't as difficult as taking it out. BTW, all those bulbs that I installed, they don't even come on at key position 2, including the rear fog lamp light. I guess they are not even wired to the system. Oh, the Rollover Protection bar light does come on and goes out. I guess that's a good thing. But I still want to know if it works.. :(

the Rollover Protection bar light does come on and goes out. I guess that's a good thing. But I still want to know if it works.. :(

If the light goes on and goes out then it passes the internal system check. Just like the airbag system, you have to assume that since it passes the check that it will work when you need it.

Thank you! BTW, I got the auto top t work again. Needed to engage the motor properly, the main center motor just did not engage right. I notice that while opening and closing, if I pull the bend top, it closes lot easier. Could this be due to needing some grease at pivot joints? Not a big deal but now it became semi-automatic because I have to give it a slight yank on it to work 100%.
If the light goes on and goes out then it passes the internal system check. Just like the airbag system, you have to assume that since it passes the check that it will work when you need it.

I ran into some of the same issues. More specifically: The top closed shut but the switch light was left blinking and the inability to open/drop the top. I found the motor nearest the left brake light assembly had been left disengaged. I reengaged the motor up by the rear of the trunk but was unaware about the other. I was unable to mate the gears on the rearward motor until reading another post explaining that dropping the top facilitated this task. In order to drop it, I had to release it from the windshield frame. Since it didn't operate, I was left stymied. Again... reading from another post gave me instructions as follow: Use allen wrench supplied with vehicle and turn allen screw(located above rear-view mirror under a small square press-fit black cap) clockwise many many times(cordless drill made this VERY easy) until top releases and folds up enough to manually drop the top into it's open position. Then I was able to open the trunk and mate the rearward motor together and not until. I then reengaged the motor a foot forward of the rear motor and all was good in the world.

I hope I was explicit enough to help anyone who might be left in the same demise I was.

I ran into some of the same issues. More specifically: The top closed shut but the switch light was left blinking and the inability to open/drop the top. I found the motor nearest the left brake light assembly had been left disengaged. ....

If it was still disengaged...how the hell did you get it to close all the way up!?

It seems alot of people play around with the emergency handle...I wonder why. My hood works fine as is (do need to retighten the tension straps) so I'm not gonna try to disengage any motors or anything. But that on a sidenote.

General note:

With the reengaging procedure, you have have to have someone pushing the storage lid closed. Without any motors at work, it will not lock itself. So have someone help you.

Rollbars: As said, the light is to check if it works. You were saying you wanted to see them work. Well I guess you don't as this means your car is laying upside down. Although they can go off if you really do something ridiculous. (I once spun out when I took a corner too fast, on fresh tyres, in the wet, very dumb I know) I even hit a stoop with the front tyre, but luckely they didn't pop-up.
You can always say: well maybe they don't work, but my point is...you can never check they like that if they work, untill a situation accures where the are needed.
Of course rollbars can be put back down.
If you'd ask something like that about the airbags...talking of which...my airbag light doesn't like up at the pre-start check, so I'll need to have it sorted out.

Curiosity - it just screams "pull me" Also, you want to make sure it works in case your battery dies right before a major low pressure system moves over your car. Possibility of that happening? .0000000001% 1 chance in a million??? I love it when you say "Tyre" it sounds so sexy :)

It seems alot of people play around with the emergency handle...I wonder why. My hood works fine as is (do need to retighten the tension straps) so I'm not gonna try to disengage any motors or anything. But that on a sidenote.