4R and E4 are not the same, just similar. You don't need the hard parts for a 4r that you would need building a E4.
For Low to Mid power a stock trans is fine, Just rebuild with Quality parts. Having just gone through this on my E4 RacerXusa had the best deal for me on parts.
Don't skimp on the torque convertor. Don't fall for the low stall gimmick or anything like that.
Use a good shift kit like a Tugger 2. You don't have to set it up for hard shift, but it does improve fluid flow and cooling. Also converts TC to on off vs PWM application.
Sonnax has some upgrades not provided by those two as well.
had read the the mechanical diode (one way clutch) in the 4R is troublesome.
New bushings are important in any trans. thrust bearings/washers is a toss up, but cheap to do while you are there.
Stake the front bushing. Watch for the correct seal material especially on the TC seal. The diesel generates too much heat for the cheap seal.
Extra clutch kits are a mixed bag as well, extra clutches means thinner plates. They don't handle the heat as well. I ended up buying the extra clutch kit just to have enough parts to get the clearances I wanted, I paid no attention to whether or not there was an extra clutch in it.
I think I updated the sprags as well just knowing they had age on them and had them fail before.
I think the 4R uses molded or bonded pistons, which are great, but you need to buy new pistons, reusing is like using a lip seal over. Not the best idea. I had the option to use those but since I wasn't having trouble already I didn't see the need for the extra $100.
I used the Racerx torque convertor. Seemed like the best deal. Good reviews. Not the cheap one though, they offer 2. They say they are built to match your truck, but I doubt that is not the case. It did however take a couple weeks to get.
A google search for "4R upgrade" will lead you down a rabbit hole but you can decide what you feel is important to upgrade. I didn't do every upgrade my trans made it 170k and still looked new inside with heavy towing and mild power improvements for most of that. It is easy to think you need all those things but you don't. Just do careful inspections during tear down and decide from there.
Since you are having a shop do it. No telling what you will really get in the end. You can't be there watching the whole process, but you would hope they have some knowledge of tear down and inspection as well as some experience with the 4R. I will say It cost me over $2k in parts alone. about $900 was just the triple disc billet convertor. Even if they could buy decent quality parts for 20% less. It gives you a good idea what kind of build you are getting based on the cost.
Anyone getting a trans built and installed for $2500, or probably even $3k is not getting the best parts or upgrades.