I'm going be completely honest with you, no matter what it is out of those things you listed they are all nightmares.
If its the water pump you will have to remove the timing belt as it is timing belt driven. don't put the old one back on. lol
the water pipe is bolted to the block with 2 10 or 12mm bolts, it just inserts into the rear of the water pump with an o-ring around the pipe. Its feels weird when you put it together but that's the way its supposed to go. same on the thermostat housing. Lube the ring when installing, it helps alot. Mine had a lot of corrosion and i cleaned it up and put it back on, well it leaked. :/ I ended up taking it apart again and replacing them. they are also cheap.
Removing the intake manifold is way more work in my opinion that dropping the ATTS unit, as half of the bolts to remove it are right above that water pipe that you cant access from the top or bottom with the ATTS unit in the way. Not to mention the entire fuel system and vacuum lines, throttle cable etc...
The ATTS unit comes right out with just pulling the drivers side axle, removing 5 bolts, connector and ATTS fluid cooling lines on top of the trans.
If it the O-Ring on the water pipe on the water pump side, and because you have an SH you will have to drop the ATTS unit in order to be able to get in there. You will have to drop the ATTS unit and remove the thermostat housing over by the distributor and slide the entire pipe out the passenger side (over by the transmission). Get the mew o-rings for both water pump and thermostat sides no matter how good they look, TRUST ME.
There are a bunch of rubber hoses back there also. 2 that come out of that metal coolant pipe and are used for the oil cooler that the filter sits on. Then there is a hose that goes from the pipe to the firewall. Those hoses are cheap.
Your best bet is to pull the drivers side axle and take out the 4 bolts holding in the ATTS unit. Once that is out start it up and find out where the leaks are coming from. Once that unit is out you can see the entire back end of the block. If you do that replace all the hoses back there because you don't want to go in there ever again
If you need any more info let me know