You might be able to go old school and put in an external volt regulator and see if it changes anything? Not sure if it would work but might be worth a try.Ford and Dodge both used them for a while.

 

ya the alternator is externally regulated from the pcm. full on no regulator the alternator will put out close to 17 volts making other things act abnormal from the voltage spike. i hate to say it but its the pcm. been rebuilding alternators since i was a kid for my dads shop know a thing or two about electrical diagnosis.

 

Oh and I wanna say that pink wire goes to the fan relay.

 

Well just an update still waiting for part .. After reading ,research, input from fellow jeep owners, mech.(thank you to all) etc.. I decided to go with a pcm.. ? I was hoping to get one from my local junkyard but as it turns out the 99 is a single year and it makes them hard to find.. I have been dealing with them for years and the beauty of that is they would let me borrow it to try it, but they do not have any, so had to purchase from another yard 75.00 and I own it regardless if it fixes it or not Oh boy 75.dollar gamble.. just an update if anybody else is having a similar problem ., hopefully this will take care of it..keep your fingers crossed mine already are!! lol

 

One question jeep did not get submerged during hurricane Sandy ?

 

Thanks for your reply.. , please tell me I did not burn up the new alternator?? I believe you are correct I think it is in the pcm have one on the way.. Thanks Bill

 

To the vets present and those mentioned by OP...i also wish you a Warm Welcome Home and THANK YOU FOR YOUR SERVICE!

Anywho, it sounds like you've done most of everything anyone would recommend here. You mentioned you've built jeeps before, so I wonder if you have any sort of electrical upgrades or modifications. Headlight harnesses, offroad lights, etc. The culprit could lie where you least expect it.

Hoping the PCM cures it for ya.

 

No thank God it does seem like it though no real corrision I went all through the harness I found the grounds located by the dipstick were broken I have a feeling this is where all the problems originated.. I have since gone over every ground and every connector on the truck cleaned ad greased everything but I think when that when ground went out it might have taken the pcm with it ? Their were actually 4 grounds at that location two were a heavier gauge wire maybe 12? and the other two were 16? and of course it looks like they end over by the pcm I think the black plug not sure have to go look.. I do know they are as important as 12v but thanks for asking lol !! we were high and dry drove my quigley van around during the storm hooking up home generators and some volunter work was very blessed during the storm..

 

Thanks no I bought it used a couple of weeks ago pretty clean except for those problems it is a nice truck, fixing it up for another nephew no aftermarket goodies on it at all.. It did have some nasty off road lights but I threw those in the garbage, removed any of the makeshift junk harness and switches fortunetley they only went off the battery but they did not even install a relay with them so not done properly have to go!! also only has factory keyless entry from jeep. everything including all lights and door switches work properly , I really do not believe anybody else was in the harness and no trailer hitch and radio is aftermarket but has adapter plug into factory jeep harness and proper ground.. So I think I should be ok after pcm at least I hope lol.. Seven..

 

Thanks again, when I say "Build" what I really mean is that I will get a jeep that has been neglected or just needs work and I go through the cooling system, brakes, valve covers , tune up and maybe a three inch lift.. I think 5 out of the 7 jeeps have 3 in lift kits this one came with a 2 inch lift kit in it already so that is as high as it goes lol.. I did with my son`s help build myself a 1997 tj wrangler with the 5.2 v-8 conversion did everything except the harness ..Had that a while I use it as a pull vehicle for the toy`s (jetski, polaris atv) but back is really starting to show it`s wear lol so taken it easy.. but still having fun.. seven...

 

Well picked up the "new pcm" basically it is exactly the same?? The only difference is The scanner is now able to communicate with the truck and it says no codes .. pass ... but fan is still not going on when truck hits temp . It will run before you start truck very strange ... It is almost like it is out of time with the key?? but even if you take ign switch off colum and use a scredriver in switch itself it does the same thing.. ?? Can the factory keyless entry be doing this it is almost like it is counting like an alarm?? about ready to give up do not know what else to try??

 

Don't give up yet mate.

You said you used grease on the ground connections; this is not desireble. Grease will act as an insulator. I recommend you remove the grease from these ground connections.

 

Thanks for the reply , the grounds I did clean with some light sanpaper on both the eye ends and the block, coil mount, firewall, and fender where they were attached I did not apply any grease to the grounds only to the connectors like the nss switch and the other two by the firewall and also in the interior any connections I opened ,inspected and put back together.. I had a friend stop by and he double checked the connections and the grounds and he felt they looked good and were makeing good contact .I did check the grounds with a light (from positive to ground) and they all showed good .. The gauges all work.. I have probally switched out the relays 5 or 6 times with know working one`s and my buddy tried it also in case I made some kind of error.. The fan will click on and off with the ign key to the on position right before start.. I can feel the Iac "pulseing "at the same time.. It is driving me really crazy not sure what else to do?? Every option ,pw, pw door locks,interior lights dash lights and turn sinals headlights, flashers ,reverse , lights all work?? .. With the key in the on position right before the start position sometimes it looks as if the gauges are pulsing with the clicking relay.. Trying to give you as much information as I can.. I appreciate any input maybe even a match at this point, lol.. gotta have a sense of humor..

 

When you say "Quigley van", do you mean Quigley 4x4 conversions? If so, you might be near me. They are based in my area around York, PA. I plan on getting a custom driveshaft from them after my lift is on.

Anywho, I'm sure you've done this already, but have you checked all the connections on your battery? I've seen weird things happen if something isn't making full contact there.

 

Thanks yes battery ends are brand new , Yes it is a quigley van from pa.. great truck I have almost 180,000 on it been all over the country in it still run`s and looks real good., I am in Long Island but my daughter went to susquehanna university and I am sure I spelt it wrong LOL !! beautifull country... Thanks for the tip I will keep digging!!