Strange clicking noise from under the hood. 6 weeks later my transmission began to slip badly?

Thank you for the response! I went back to the shop today to inquire about some of the info on the invoice. The mechanic also told me that my auto will need to be continually flushed every few weeks indefinitely, unless I purchase a new engine or transmission. He admitted to making a mistake for charging me twice for a radiator cap, $22.00 the first time and $42.00 the second time, which he refunded for me. I am not satisfied with the way I have been treated by this auto shop. A friend who came with me asked the head mechanic or manager, im not sure which he is, maybe both, he asked why was my vehicle flushed a second time, when my auto was brought in for transmission problems? The mechanic told me because it needed to be done and when they drove my auto around, they experienced no shifting issues. I had extreme transmission problems before the first time I brought it in and after they said the shifting issues were resolved. Is it possible for him to be telling me the truth about this?

It was the coolant system. Also, before I had the radiator replaced and the hoses, my transmission ran perfectly fine with absolutely no problems, no noises, and no strange sounds. As soon as I got my auto back from the radiator repair, I suddenly had strange noises coming from under the hood and my auto has not been the same. My friend brought up the head gasket problem and the mechanic said that it was not the head gasket. I don't remember 100% what he said about oil, but he did say something about there being oil and so this coolant flush would need to continue. It did seem bogus to me as well, because they basically replaced the whole coolant system, radiator and hoses, and flushed it once, so why would it have to continually get flushed? I am definitely not going back there again. I wish there was something more I could do to warn other people about this place and their shady ways. Maybe write a complaint to the BBB, I don't know. I almost feel like something happened to my auto while it was in the shop to cause it to break down so much all at once. The miles are high, so it could just be natural breakdown from age.I will def take it to a transmission shop and get an estimate on what the problem really is.

I know what happened to your escape and yes you can prove it unless the shop corrected it.
Follow along closely but this will make complete sense and the mechanics mistake may still be obvious.
You said you had the radiator replaced, this is how it starts.
On the radiator on the driver side tank at the bottom there is a large hole for the water hose from the tank to the engine block. Above that about 2 inches there is another inlet, this one has a small hose attached and it comes from the transmission and it is the transmission fluid cooling line inlet, (inside the plastic radiator tank is a brass set of coins that the fluid runs through while the water in the tank cools it. (Now pay close to this part) directly above that cooling line inlet is another inlet. This inlet goes up to the bottom of the radiator fill tank and coolant travels through it. The important thing to note is both the tranny cooling line and that coolant line are the same size rubber hose about 3/8 I think they both slip over the nipples on the radiator tank and the only difference is one is brass and one is plastic. Lastly there a transmission cooling line return at the top of the radiator tank that goes back to the Trans. For a total of one big hose and three smaller hose connections all on the driver side.
Go look on your escape and you will see those hoses connected 4 in total the bottom ones are hard to see. Now here's what happens when a mechanic isn't paying attention to where the hoses go when installing the new radiator. The two 3/8 hoses on the bottom are easily switched without any problem and this is what happens.
When starting the vehicle the Trans line will pump tranny fluid into the radiator (the reason they had to flush your coolant system?) It will be a mess of oily fluid and coolant.
Also in turn the radiator coolant hose attached incorrectly to the Trans cooler will put coolant into your transmission. The coolant will not pump into the tranny as fast as the Trans fluid pumps into the coolant system but it will introduce coolant into the transmission system within a shirt time. (Possibly the reason for the low coolant light on the way home?) Thus destroying your transmission by introducing a continues amount of coolant into the Trans fluid lines and Trans.
I hope this is all making sense. I know if you physically look at your radiator and the hoses on the driver side you will see exactly what I am explaining. The only way to know for sure if the mechanic shop figured out there mistake and corrected it is to trace the hose from the radiator to thier destination. You will have to remove one of the smaller 3/8 hoses at the bottom to confirm wich is wich remember I stated the hose from the tranny slips over the brass nipple from the radiator and the hose from the coolant fill tank slips over the plastic nipple.
My expert opinion is that the mechanic mistakenly switched the two hoses without realizing it. The only symptom of the hose switch is lots of transmission oil in the coolant system making it very oily and with obvious oil in the coolant. And it will keep pumping it in at a high enough rate it should be puking out the coolant overflow in short order also leaving a oily residue underneath the coolant fill tank on the engine and engine compartment. There would be so much Trans oil in the coolant that a flush would help clean it but one coolant flush won't be enough and could explain why they insisted on many more coolant flushes in the future.
I offer this information from personal experience as a shop foreman at a Ford dealership for many years. I witnessed this hose switch on more then one occasion by several very good mechanics that just weren't paying attention because they are the same size hose and right next to each other.
I often wondered how many Ford escape were destroyed by this simple hose switch mistake I knew of two and yours makes three now. My guess is it's into the hundreds because Ford escape radiators are weak and break easily so replacement is often needed in around 100,000 miles give or take some. Ford changed this design flaw in later years but I believe it is this simple design flaw of placing these lines so close together that gave the 1st Gen Ford escape tranny a bad reputation. If I could make a wager this is what happened to yours I would wager $1000 with no worry of losing.
If you chose to look into your radiator hoses as I have described make sure to video what you do and if the lines are still switched you will now have the hard evidence you need to prove the mechanic shop was at fault and negligent in the installing of your new radiator. Good luck towguy