There are 7 different output shaft styles for the 700R4 or 4L60. There are 4 different lengths as well. The input shafts are either 27 or 30 splines, depending on if they are early or late model, and if you are putting it behind a diesel, you will need the 30 spline, or late model, as the 27 spline / early model is known to crack behind the torque of a 6.2 litre.
As for the flexplate, most of the ones I have seen are slotted to accept all six bolts, so that should not be an issue. You will need a 12V supply to your lockup solenoid, or the torque converter will generate too much heat in overdrive, and will turn your ATF to pudding over time, and kill your transmission.
I prefer to wire the valve body so it will go into lockup only in overdrive, or 4th gear. This saves the clutch in the torque converter by not having it disengage and engage with 2nd and 3rd gear, where it is really not needed. There is also a way to modify the valve body to go into lockup only in 4th gear at speeds of 55 MPH or greater via hydraulics, which nullifies the need for a 12V supply to the trannsmission.
The TH400 is truly the easiest transmission in the universe to rebuild - even easier than a TH350, believe it or not.
You will have to drill extra holes in your frame (x 4) if you change from a 3L80 (TH400) to the 4L60 (700R4). You will also need a transfer case with passenger-side drop off either another 4L60 or 3L60 (TH350), as they have the same spline count, but are totally different than any of the TH400s.
If you decide to go with the 700R4 switch, which will work nicely with 3.08:1 gears if you adjust the governor correctly (springs & weights), and you can't find a transfer case for one, PM me and I will see if I can help.
You will also want a diesel 700R4 torque converter. They no longer make the 6-pad type, and that is ok. The reason they made them with 6 pads in the first place was the diesels were ripping the pads off of them with 3 pads because of the way they were brazed onto the front. They actually changed the welding pattern and found 3 pads were enough. I recommend a GM33 torque converter for your application. It is found in the '94 - '97 PWM (Pulse-Width Modulated) vehicles. PWM was used to avoid a harsh engagement of the lockup apply, which kept down customer complaints. Since it generates a little more heat vs. a direct, single pulse engagement, they switched from a paper friction to a low-carbon semi metallic friction for the torque converter clutch. It also has the best stall speed for the 6.2 diesel at about 1400 - 1600 RPM. If you need one of these and everyone you talk to wants a whole bunch of money for one, PM me and I will see if I can help.
I like to remove the check ball in the end of the input shaft, which causes a softer apply at lockup if left in, and run the GM33 as a sort of HD modification. While it is never good to have a hard bang of a shift in any gear or with the lockup apply circuit, soft shifts or applies are where the heat increases, and also when the most wear occurs on the frictions and steels. Think of it as if you slowly let the clutch out on a standard transmission with each take-off or shift, versus shifting normally and quickly. Which way would burn out the clutch faster?
Also, if you put in a 2nd and 4th super servo, which can be done without having to take apart the inside of the transmission, you can then safely tow most moderate loads in overdrive with your 4L60. You just have to be able to take out a big snap ring that holds in the big round servo cover on the passenger side of the trans. If you have any questions and would like to talk directly to someone who has been building transmissions for about 15 years, please do not hesitate to PM me. BTW, the 700R4 is my favorite transmission to build and modify.