Yes and no...
The AOD-E in the '92-'94 Crown Vic/Merc Grand Marq and the 4R70W in the '95-'01 Crown Vics and Marqs are electronically controlled.
The TC shudder always occurs as a breakdown between the oil/friction material interface. The reason is partially due to a faulty designed TC.
The TC locks up when commanded via the EEC-IV or EEC-V (depending on the year model). It gets a signal from the PCM and energizes the TCC (torque converter clutch) solenoid. The signal is a pulsation type rather than an "On/Off" signal as in the trucks. This helps contribute to the shudder.
Anyway, the piston moves forward to lock-up the torque converter. The way the converter clutch piston is made is, it only contacts the inner diameter of the friction material. With the pulsation signal and the the piston only using the outside edge of the friction material, it wears prematurely. This breaks down the fluid and causes the TC to slip. The slipping generates lots of heat.
So, as you are cruising on the highway and you tip into the throttle to pass...the shudder comes on. It happens in 4th (overdrive) and 3rd gears. It can also occur on the 3-4 upshifts and eventually on the 2-3 upshifts.
It will never happen in first gear and almost never in second gear as the PCM won't command a lock-up that low. Be aware that driving around town in third gear to avoid the shudder in 4th can aggrevate the shudder even more.
The cure is a new Ford or aftermarket TC. The newer designed Ford TC's have a larger, stiffer piston. The friction material was also increased to help fight this problem. The band-aid for this shudder problem is to simply drain all the old fluid out (TC too) and install a new filter assy and MERCON-V ATF (p.n. XT-5-QM). Then install a good plate style transmission cooler (p.n. F8VZ-7A095-AA and install kit, p.n. vary depending on the model year). See TSB 98-8-7 for more details. The shudder will not return for at least 25k miles. You should change your fluid at least every 20k miles. If you want I can explain why. Anyhow, MERCON-V is the important part here. TSB 98-8-7 actually states: FLUIDS LABELED MERCON-V ATF ARE RECOMMENDED FOR SERVICING 1992 AND BEYOND AOD-E/4R70W TRANSMISSIONS WHICH ORIGINALLY SPECIFIED MERCON SERVICE FLUID".
The shift kit will not rectify the TC shudder. Although a new '99 main control (valve body) will allow more lube to the converter clutch circuit. There is an man by the name of Jerry (www.tccoa.com
) who can custom burn you a chip to eliminate the TC shudder as he changes the lock-up schedule in the EEC. He also does a few extra changes for the better if you know what I mean. Jerry knows more about AOD-E/4R70W's than anybody else...after all he engineered them.
So the answer is...short term correction is MERCON-V and a plate style cooler (ie Ford, B&M, Hayden). Long term is a new TC.
I believe your clunking between 3rd and 4th gears is due to driveline components such as worn u-joints. Check the fluid level as well, but ATF cannot cause such an audible clunk (that is felt as well) and the TC would be damaged to do that.