Over the years, I have had ATS kit and a Suncoast GM5 kit. I have seen the photos of the PPE kit. DONT GO ATS!!!! I'm currently running a GM5, with other internal mods, and an ML Precision converter. The combination works great.
In my opinion these are "kits" to increase the performance of your trans. These are not what I would call a rebuild kit. All seem to come with the gaskets, or more gaskets than you may need if one of the suppliers includes gaskets, then throws in a complete Trans-Go package, which will also come with gaskets. What these do not provide are the internal seals, o-rings, etc. That is an extra box. They also will not provide the torrington bearings, which should probably be replaced.
As has been stated earlier, either the Suncoast or PPE kit are a good start. I would also ask your builder if he uses a Tech II for resetting the taps and fast learn the TCM. Allison also makes a box that plugs in and can reset the taps and fast learn the transmission. The TCM should REALLY be reset with the correct tool. I have heard that other units (Snap-On, EFILive) can work OK on some transmissions, but not others, I guess it depends on the TCM or transmission series, or both....
Mike L's cooler is the way to go. I took off my deep pan on the last rebuild, because I got tired of paying for more oil that is just not needed. The deep pan was my first try at cooling the trans. It did not work, it just took longer to heat the oil. The cooler fixed the issue.
I'll leave the converter discussion to others.