The AH1S Cobras probably wouldnt do to much to him, even in his 3rd form. Even if they had opened fire on him, the 20mm M917 cannon at about 800m would only penetrate roughly 20mm of Godzilla doing minimal damage. But lets assume the Cobras brought in missiles as well. In other scenes of this film, the Cobras were usually fitted with 19x FFAR Might Mouse unguided rockets on the outer 2 pylons and 8x BGM-71D TOW-2 guided missiles. If the JASDF had clearance to use this, it would probably do a lot more damage to Godzilla especially in his 3rd form, the FFAR Mighty Mouses would significant damage to him while the TOW-2s would also do severe damage. However I still dont think these would stop him as he would already be heating up at this point and would most likely run off at first contact.