I just went thru something similar.
One of the A.I.R Trees rotted out from the inside and required replacement.
Twisted off two of the 4 nuts and had to machine out the thread (Nut) while not intruding i.e. damaging the manifold.
I used a series of drill bits up to the correct tap size and pulled the 'treads' of the nut out of the manifold holes,,,
then purchased (appx 40$ ouch) a 1/4-18 NPSF 4FLT STR D/S Pipe tap from Fastenal (pn 16356 Brand Greenfield Tap & Die) and chased my manifold thread for a clean fit on the new tube nuts.
P.S. also machined some custom hidden plugs that seat below the tubes as my pump is de-vaned and need to seal exhaust gases from the check vlv etc.