I have a 1996 windstar, 3.8L.
I faced the transmission issue at around 100K miles....back around 2001'ish.
I did a LOT of reading online......found that folks who save money (up to 1/2 the cost of FORD) were looking for another transmission just over 1 year later....and were unhappy folks.
I paid about $2860 for a genuine FORD remanufactured....installed.
At that time the warranty was 2 years 75K.
The key thing that they do is apply all the updates during the process.
By 2000, they had ironed out many of the problems (lubrication, etc).
Many "rebuild" shops just fix what is wrong....broken.....and don't do the updates.....or replace many wear items.
It is all about price.....
My FORD replacement really hurt the wallet......but I have NO regrets......it has over 100K on it....
Instead of taking it in for a fluid / filter service every 30K, I now do yearly (around 15-20K miles) fluid exchange, filter every other year.....I use Redline D4 fluid, and installed a auxillary transmission fluid cooler...and a Magenefine inline filter.
There are other quality ATF fluids out there.....make SURE that it meets the Mercon V specification.
I have read that Jasper also does the updates......but like OEM, you are going to pay for it.
If one plans to keep the vehicle....I would get the "top shelf" remanufactured unit that you can feel confident in.
Make SURE that you keep that fluid changed AT LEAST every 30K miles (21K for "severe service) with a quality fluid that meets the Mercon V specification.
FORD has also issued a couple of TSBs about the transmission fluid cooler (all have the in-radiator cooler) becoming clogged or partially clogged......restricting fluid flow...causing the new transmission to fail due to heat.....
Also they warn about the crud in the cooler contaminating the new fluid....also leading to failure of the new transmission.
For this reason......I would ask them to follow TSB # 3-14-8 which gives the transmission cooler flushing process instructions.
Also ask them to flow test the cooler to make sure that there is no obstruction.
If flushing does not result in the correct flow.....the in-radiator cooler must be replaced.....which requires that the whole radiator assembly be replaced.
For what it is worth..... I now have over 210K miles on my '96 windstar..... Hoping for "a couple more years".