I figured out that we need only two pins to align the subframe.

Right side alignment hole.
there is a matching hole on the left side.

any idea where we can find the specs for these pins?

it seems that dropping the whole engine and subframe is going to become routine maintenance for me since it so much simpler to work on the engine and transmission when it's out of the car.

 

The hole you're asking about is used by the support jack to lower the subframe, its not used to align the subframe to the body. You can just drop the subframe on its own without the engine and transmission on it. What sort of repair are you doing?




Install the special tool.

NOTE:
Left-hand shown, right-hand similar.




Position and adjust the special tool rear height adjuster.
NOTE:
Left-hand shown, right-hand similar.




Remove the front subframe reinforcement plate retaining bolts.
NOTE:
Left-hand shown, right-hand similar.




Remove the front subframe rear mount retaining bolts.

 

If if you read just before that sequence the illustration shows 2 alignment pins.

the Haynes manual mentions the pins and a couple other jtis manuals mention them as well.

i think the rear height adjuster goes over the pins and retains them.

How misaligned can you get without those pins?

i need to check the timing chain, clutch transfer case seals, gear box selectors, engine block seals, sump gasket and overhaul the front struts.