I developed a TC shudder at 58,000 mi. and the dealer flushed and filled the trans. It took 14 quarts of Mercon 5 and it cost $150. They said it would clear up in about 100-200 mi. 2000 mi. later, I still had the shudder.
The dealer said this was a drivability issue, and there was no damage or impending damage to my vehicle. I am worried because I have about 5K left on my Ford Extended Warranty.
THe shudder happens only in OD in the highest gear @ 40mph and 1300 rpm's. Uphill, downhill, flat, it doesn't matter. It feels like I'm towing a trailer with the wrong ball. I have the 4.6, 4R7W or whatever trans and 265/75/R16's.
I bought a product called Lubegard at Napa. There's a green box just for Mercon V applications. I added it today and I'll keep everyone posted. I know I'm not the only one out there with a transmission that suffers from epilepsy.

 

My Wife's 97 T-Bird developed the shuttering at 39K
I took it to a dealer who did the flush and fill of all 14-15 qts of fluid. Fortunately, it took care of her shuttering completely.
Our car was out of warranty. BUT being as you have 5K left on the waqrranty, and you have already done the flush and fill,
I'd be fighting like hell to get the trans replaced. Of course they are going to stall you, until your just over the warranty period.

DON'T LET EM DO IT TO YOU!!!!!!

 

Try Lube Gard Products out of Washington state. Works wonders!!

 

As long as you started having the problem diagnosed before the warranty runs out and they haven't fixed it yet, it shouldn't matter. I had a '93 Ranger with a 3.0 V6 that was burning oil. I got Ford to look at it before it ran out of warranty and they kept track of how often it needed oil. 5K miles after the warranty was out, Ford rebuilt the engine.