I installed an aod transmission on an 88 cougar and I have everything hooked up and it will not engage and spin the tires. what could this be

A4OD

Transfer Case - Mechanical Shift On The Fly (MSOF) Operation The mechanical shift on the fly (MSOF) system is a manual shift 4WD system that allows the operator to chose between two different 4x4 modes as well as 2-wheel drive. The operator can switch between 2WD and 4H mode at speeds up to 88 km/h (55 mph). To engage or disengage 4L range, the vehicle speed must be less than 5 km/h (3 mph), the brake pedal depressed, and the transmission must be in NEUTRAL.
Shifts between 2H and 4H can be made at a stop or any forward speed up to 88 km/h (55 mph). At temperatures below 0°C (32°F) shifts should not be performed above 72 km/h (45 mph).
The transfer case is equipped with an electromagnetic cluch which is located inside the case. This clutch is used to spin up the front driveline when shifting from 2WD to 4x4 mode at speed. When the manual shift lever is moved, this activates the 4WD indicator switch, 4WD electric clutch relay, and the electromagnetic clutch. When the transfer case front and rear output shafts are synchronized, the spring loaded lockup collar mechanically engages the mainshaft hub to the drive sprocket. Finally, the front axle collar is engaged and the electromagnetic clutch is deactivated.

Pull it out ,strip it and go back over what was done

It wasn't assembled or built correctly,period

re adjust the cable per the shop manual.

Timing chain, and transmission.

No. AOD trans from 1985 is hydraulic shift. You need to hook up the Throttle valve cable from the drivers side of the trans to the carb. Is this hooked up.

According to Haynes Auto Repair Manual, section on automatic transmissions, the 1994 Towncar has the AODE transmission
Baumann Electronic Controls website
URL: http://www.becontrols.com/tech/ch1alphabet.htm
has following:
The Automatic Overdrive (AOD) transmission was introduced in 1980 as Ford's first four-speed automatic overdrive transmission.
The AOD-E transmission is essentially a beefed-up electronically-controlled version of the AOD.
If this doesn't answer your question, you might troll around the website.

the model of the trans is "AOD"

if it is just the steel line you can cut it and reflare the end

you can get it from 88 ford tuderbird.