I would definetly take it to a good Ford dealer as they have had alot of experience with these over the years and should be able to identify your issues easier than a mechanic not so proficient with these transmissions. Where are you located?
As for the clutch kit, they retail for around $1000 and $70 for the necessary seal kit, but can help getting the price down for you if need be (just PM me if you need additional help). You may need a few extra bits here and there but you wont know until the job is being done.
If its a
TCM issue, your car is still under the component extended warranty which should cover that if its the problem - again another benefit of going to a Ford Dealer.