For the past few months, the one touch down wasnt working, neither was the cruise control.
Came back from the shop and randomly the cruise control was working. one touch down is still not working.

I was told that the GEM or JEM module needed to be replaced. quoted over 400. NOT A CHANCE. i will live without the one touch down. i also noticed there is a fuse/relay for the one touch down. may replace that.
MORE IMPORTANTLY
I told them them that there is a clunk in the front suspension, especially when turning or going over bumps.

They attributed it to my sway bar links not being tightened to spec. I believe i put them down to 45ft/lb. would this actually cause the noise or are there more likely suspects? i've lost trust in this shop as of my last visit. both upper and lower control arms were replaced about 2 years ago.

 

Ok, while the GEM module might need to be replaced, you should check the grounds, bad grounds can cause lots of systemic electrical problems.

A clunk can be caused by sway bar links, rarely does tightening them resolve it, if the link clunks, it needs to be replaced. Sway bar links are usually fairly inexpensive.

Just because you have control arms replaced doesn't mean that other things can't wear out, nor does it mean that quality replacements were used.

What is one touch down?

 

Sway bar links are 3 months old.

One touch down is the Auto Down function on the drivers window.

What grounds might affect the GEM?

 

You never mentioned a year or model. This info is for the 3rd Gen (02-05) Explorer/Mountaineer.

I had similar electrical issues with my 02 xlt. The dome lights would stay on until the battery saver feature turned them off, the accessory delay wasn't working, the driver side puddle light didn't work, the keypad on the door would set off the alarm when I pressed it, the door ajar light would flash and beep at highway speeds, the radio would shut off as soon as I turned the key off, the delayed accessories didn't work, etc. The alarm would beep twice when I armed it. Recently all 4 windows stopped working. Most recently the driver door lock actuator stopped working.

A lot of electrical issues can be traced back to broken/damaged wire(s) in the boot between the body and the driver's door. I found 3 broken wires and repaired them. The thin black ground wire was broken and after repairing it all was back to normal. When the windows stopped working, I repaired the thick black ground wire and the windows now work like a champ. I had to repair the pink/black wire to fix the driver door lock actuator.

Here is the thread for removing the door panel: How To: Remove/Replace 3rd Gen Door Panel - Ford Explorer Ranger Enthusiasts "Serious Explorations"®

Here is a great thread for checking for broken/damaged wires, thanks to synyster for this awesome write-up: How To: Fix the Door Ajar Problem - Ford Explorer Ranger Enthusiasts "Serious Explorations"®

Be sure to take your time when looking for broken/damaged wire(s). Check all the wires for breaks/damage. When you think you're done looking, look again, and again, and again. A bright flashlight can be very helpful.

If all else fails, here is a great link for troubleshooting the power windows, thanks to theofam for this great link 2002 Explorer Power Window System Diagnosis

Here is the thread for checking relays: How To: Test a Relay - Ford Explorer Ranger Enthusiasts "Serious Explorations"®

Hope this helps out. Good luck!!

 

Your profile states that you have a '96 EX. Don't know if this will help or not, but I had a 'clunk' for approx. 8 years that I tried to localize in my suspension system. The shops I took it to cited everything from the wheel bearings to the steering column bushing.

About 3 months ago, I took the shroud off of my steering column to try to localize the 'clunk' myself, and found that the heavy horn plate had 2 rubber standoffs that were actually broken, causing it to 'clunk' in the steering wheel with every turn and bump. A little super glue and she's been perfect and silent (just like a woman should be). LOL!

Don't know if the 2nd gen Explorers changed the horn setup, but if not, this could still be suspect for yours.

 

Sorry, i suppose since i was on my hiatus from the forums, they decided to switch **** up and removed my profile info. 1996 4.0 XLT explorer