It looks like you didn't post the brand name or manufacturer of the power supplies. That can make a huge difference in getting help and identifying the problem.
You need to see if the power supplies will work without any load on them. Use the paper clip in the motherboard connector method (examples abound, do a search for the details) and see if the power supplies power on at all anymore. If they do, use a voltmeter to see if it produces 12v on the required pins in the different connectors. Also look at the specs for the power supplies to see if the 12v supplied is on a single or multiple rails. You need single rail. Cheaper power supplies generally are multiple rail which will cause you problems.
After you determine if the power supplies will power on at all, then open the S3's and see if there are any obvious burned components or traces on the printed circuit boards. It sounds like the power supply leads/traces may be fused into a short and that may have popped/trashed your power supplies. If there is any obvious internal damage open a support request with bitmaintech and work with them to see if it's a warranty repair or replacement situation.
Just a word for the future: you're spending lots of money on a piece of equipment... don't scrimp on the power supply to run it, especially when sellers such as newegg.com have perfectly functional power supplies for reasonable prices and frequently offer rebate or discounts that make the power supplies even more reasonable in price. Look for at least a 500 watt power supply with the 12v on a SINGLE rail, not multiple. For a comfort margin and to operate the power supplies more efficiently, you may want to get a minimum 600 watt power supply. Just as a personal preference, one power supply per miner and I generally use CX500's or CX600's or even CX750's, but not the modular power supplies (they generally have 1 pci-e connector and you need 2 or more if over clocking). If you power multiple miners off a larger power supply and it tanks, you have multiple miners out of service.
Yes I'm aware of this. The first 1 was a power supply claimed from an ancient computer. The 750 was a CHIEF MAX 750. I returned that. The 1000s were Kentek. I am not sure what happened to the first, it just smoked and stopped. But the fuse was good. The second one blew a fuse, so I unsoldered the good fuse but that went as soon as I plugged in with no load. So those ones are no good at all until I can get new fuses for them. As far as opening the cases, I did that and everything looks fine. Nothing visually wrong at all. I even went as far at to test for continuity in all the cables, very tedious. As far a Bitmain I am in contact with them. But progress is slow. I now have a modular PSU so each blade gets it's own rail. Also, The one that blew the three got so hot there's still pieces of the pin glued to the connector. I tried using both controllers in each miner and the results were the same. Nothing. I'm not sure if I should be asking for new boards or whole new units. I just want to mine some coin!
Can you link to the exact 1000W PSUs you used please?
it looks like he used this one..
http://www.amazon.com/KENTEK-Supply-EPS12V-SLI-ready-PCI-Express/dp/B00596TJU2/ref=sr_1_4?s=electronics&ie=UTF8&qid=1420286116&sr=1-4&keywords=KENTEK
very poor rating, not even 80+
has 2 12v rails rated at only 35A, so if he plugged the 2 miners into the pci-e slots he overloaded the psu as soon as it powered on.