The odds?
Zero.
Zip.
Nada.
Machine tools are notoriously difficult to destroy by bombing. In fact if one looks at the BDA photos taken by American photographers after the attack one of the striking things is the sight of machine tools staging in the burned down hangers that had once housed them. This was also demonstrated time and again by the CBO in Europe, and close review of the aftermatch of the major firebombing attacks against Japan will show machine tools have survived the firestorms. Undoubtedly many tool would receive damage, especially to power cords, handles, etc., even to motors if the heat was high enough, but the actual tools, not so much. It would require actual close contact with something like thermite, which the IJN bomb inventory totally lacked, to do any actual damage to the machine tools.
Dry docks are also quite difficult to destroy by bombing. Had there been a sufficiently long clear path it would have been possible to try to use torpedoes to destroy the dock doors or even the floating dock cassions, but given the layout of the harbor those did not really exist. The attackers did take numerous shots at 1010 Dock, all failed
The fuel tank issue has been addressed so many times here that it is almost a meme. Fuel tanks are very difficult to destroy, being a fairly small target, especially for a level bomber, each tank was bermed, limiting splinter damage, and not a tenth as flammable as some folks imagine (fuel oil is about half a step over road asphalt, is as viscous as 35F molasses, and is surprisingly difficult to get to burn, drop a lighted match on it and the match will snuff out).
All the targets were also increasingly difficult to see as the raid's two strikes continued, thanks to smoke from the fires (both structures and things like paint, diesel, gasoline, and some fuel oil that was ignited by things like burning gasoline.
Lastly, the infrastructure of the base was, quite literally, the last thing on the target list provided to the Strike Force. There were still several battleships afloat (trapped by their sister's who had floundered after torpedo hits (both Maryland and Tennessee were damaged but combat capable with reduced effectiveness immediately after the attack; both went under their own power to Puget Sound for repair/refit and were back in Hawaii in a couple months. Pennsylvania, which was IN 1010 dock, took one bomb hit that wiped out one of the 5/25 guns, and was ready for sea as soon as the dock entry was cleared and the three shafts that were being repaired were reattached; she sailed for the West Coast in December 20th, again under her own power and was back at Pearl in about 10 weeks. If the Japanese had gone back for a third strike those three BB, all of which were continuing to fire throughout the attacks, making their operational status quite evident, would have been the primary targets of any third wave, followed by the numerous heavy (New Orleans and San Francisco, but under routine repair but effectively undamaged in the attacks) and light (Detroit, Phoenix, Honolulu, St. Louis) cruisers in the harbor and either undamaged or only lightly damaged. After those ships the next priority would have been the TWENTY-FIVE undamaged destroyers and 4 undamaged subs (although these would probably have been well away and hunting the task force before the fifth or sixth wave of attacks reached them on the targeting list somewhere around the afternoon of December 8th.