Servo's could be bad if the rebuilder did not replace. They are like $8 parts, so replace them.
Issues are most likely due to EPC circuit pressure issues in the valve body. When the trans warms us, the fluid viscosity changes, and valve clearances change. The 4R's / 5R's are known to have multiple valve body issues. Perform a wet/air test on the VB while VB is still bolted to the case. Will tell you where the VB may be leaking.
The VB should be gone through with a fine tooth comb. Very easy to mess up a plunger orientation, spring location, or retainer location.
Transgo and Superior kits are worthless for these valve body's. Use the Sonnax updates and Ford updates available for them.
Also find out what parts your rebuilder replaced in the trans. $400 is really cheap for parts/labor. Rebuilt VB's can cost over $400 alone. A typical quality rebuild for the A4LD/4R/5R will have $500-$600+ in parts, including a reman torque converter, frictions, steels, gaskets, seals, new bands, servo's, sonnax updates, Ford updates, etc. This doesn't count any hard parts that may need replaced. If the total parts/labor was $400, i can guarantee that the "rebuild" was skimped.
Brett