it was garaged for 89k miles we obtained it in 2018 and its been dealer maintained since new all records everything works No rust holes anywhere. It does have a slight headliner issue but only up against the windshield and it has not spread. The radio lights also do not work but other than that, it ran strong and smooth. it had all plugs changed and all coils done at 120k. trans is smooth. No dings or dents but the one clip on bumper needs replaced as well, it sags about 1/2" but thats it. we believed the motor would last us 200k minimum the oil is always clear even when we change it.
I am still not sure how many miles are on it now. I will assume around 120k miles since you have only owned it for 2-3 years and bought it with less than 100k miles. I think you are in a position where you should consider looking at repairs like wheel bearings, radiator, accessories (water pump, AC compressor, alternator etc.) and any other parts that can typically need replaced by 150k miles. Has the transmission, differentials, transfer case, brake, coolant, power steering fluids been replaced? At 120k these fluids all should be replaced if you want to get a reliable 200k miles out of the vehicle. Especially the transmission and transfer case. The transmission is way overdue for a pan drop, filter change and refill if it hasn't been done. Don't believe Ford's recommended service intervals for fluids. They only insure they get repair work after the warranty expires. The things I just mentioned all cost money and it is likely you will need to address them at some point.
If I were in your shoes (and I was last fall with my old 2002 XLT) I would add up the cost of the engine, the fluid maintenance items you might need to have done, replacing the radiator (they are notorious for leaking (I had to replace mine last fall), a couple of wheel bearings (you are at the point they start to fail) and then throw another $1k in the sum to cover a few of the other items that typically go wrong that I never mentioned. Keep in mind that I never even brought up a transmission repair or replacement but the 6R60 is fairly reliable if the pan is dropped and fluid refilled every 40k miles. Add in your engine replacement and you are looking at the cost of driving this for another 100k miles. The good thing is the engine should go to 300k+ miles if you install a remanufactured one.
Last fall I did what I mention above regarding my 2002 XLT with 116k miles. I expected the engine to last to 200k and beyond because the 4.6L 2V engines are darn near bullet proof. I knew a transmission replacement was coming soon because the 5R55 is almost guaranteed to die before 150k miles. It needed some other repairs like front wheel bearings, headlights/tail lights (they let in water) and a few other things. After adding up the anticipated costs I decided getting a newer model was the better choice. I ended up buying the 2010 Mountaineer I have now for around $6,500. It has every option available for this year, had a little over 100k miles on it, was completely rust free and in pristine condition with all things working. It had a decent maintenance history, the Carfax said it spent no time in the rust belt and even the retractable running boards worked. I replaced the radiator (and water pump as a preventative measure), installed new tires and replaced all the drive line fluids. All in I spent $8,500 ($6,500 + $2,000) and have what I believe is a fairly reliable SUV. I know there will be other repair bills to come but hopefully they will be minor and spread out over many miles and several years.
So I advise you to see what your $5k repair budget along with some of the other maintenance/repair costs would give you to apply to purchasing a newer vehicle. You might find it is better to cut bait on this one and replace it with something newer and with less miles. Or you might find keeping this one is the better choice.