Do you have a volt meter? It's probably not that bad. Don't see any wires that turned crispy.
There is a rectifier under the area you are pointing to. If you had a short down stream the rectifier will act like a fuse and burn out (smoke). The blocks for your red wires and black wires (for gecko power) are butted right against each other. The buss bars you screwed into the top could touch each other. I put a spacer between mine just to be safe.

Get a volt/ohm meter and we can check some things. Free Harbor Freight one is plenty good.

That does not get enough mention for newbies imo. Too many first time electricians wire everything like on the forum and flip the switch hoping for the best.
I know this is no help to you now, but since a lot of money goes into the electric part of an MM what I did is wire everything, then take it apart, as in, unscrew the vital connections, and really go step by step ( first PSU wiring triple check, then power up - test voltage, on to the next. I catched 2 very stupid mistakes ( very unnecessary basic ones - caused by wire mismatching ) while I was 100% sure I wired everything correctly, which could have cost me a drive and a fried input/cpu. Especially since you probably won't wire everything up in one day, mistakes like this can happen quickly when you are working on and off on (electrical) projects. I always doubt myself nowadays, and it has saved me lot's of money ( but costed me even more before when I was too sure of myself ).

Anyways
For your situ, go fault finding step by step. It makes things more comprehensible, especially when you're on unfamiliar territory. So unscrew/disconnect vital functions and do as above. Start with checking the PSU wiring, while it's disconnected, and when you're pretty sure power it and test the voltage, everything ok, next part of the circuit (rectifier etc etc).The culprit will be isolated and show itself before you can do more damage.

Hi John. Thanks for the response. I just bought a voltmeter, and have disconnected the outbound DC wires. I have installed spacers between contact blocks for the AC going into the transformer. I just switched on the power again, and I get smoke right at the base of the contact block above the rectifier.

I have ordered a new rectifier module from Antek. The only thing I can think of to check is the AC going into the transformer after I disconnect it. I do have single wires from the contactor jumpered to each pair of transformer leads with a contact block.

You need to slow down a little. We weren't ready to turn on power again. We need to understand what went wrong with the initial turn on. Once the Rectifier is smoking it can continue to smoke until it is replaced even though you disconnected the initial short.

Unplug the power for now and leave it disconnected. At least until we make some measurements.

You have disconnected the DC Output of the power supply going to the Geckos. Set your meter to Ohms and connect the leads to the 2 wires you disconnected from the power supply. You will be seeing what the power supply saw. Let me know what you read.

When you get the new rectifier, mark all the wires connected to the old one and take a picture. You need to be positive that you connect the new one without crossing a wire. If you do it wrong you will have two problems and nothing will make sense.

Could you possibly show a closer view of the problem area and the bottom of the board?

Problem solved
 

Thanks guys for suggesting the multimeter. I had a friend check my work and he verified I fried my rectifier. Good thing I had a new Antek regulator Fed-Xed. We installed that, rerouted the 12v power so that it was rectified too(his suggestion), checked resistance on all the connections, and hooked up a variable power supply(24v .75amp) to test things under a load that wouldn't fry anything. We found a dead short in the terminal blocks for the power to the Gecko's. All it took was a spacer to solve the problem, and then, "Bob's your uncle!"

I hooked up the PC and ran the setup for EMC2. I got an error message, so I think I'll upgrade to a newer version using the latest Ubuntu LTS version and the newer EMC that works with that. If that doesn't work, I guess I'll have to swap in a WIN7 machine and Mach - Oh how I hate Windows! The only nice part is my friends industrial automation company uses it, so I'll have plenty of in-person support.

I'm a lot closer to making dust. Just need to connect the motors and tidy up a few items, and I'll be good to go.

Glad you found your problem. I can relate to your Windows "issues", I have been pulling my hair out over an Asus laptop running 8.1 (which I HATE). But can't seem to get Win 7 to install, they make it very difficult!
Sorry for the rant :o
Best of luck on the rest of the build...sounds like you are close!
Mark

I hated Win8 but have found a new found love for it once I accepted it was a new direction. I don't know how Mach would run on it but I know it will run on Win7.

I know it is a new direction, but I cannot help but feel the direction is leading me off of a cliff! :)

Trust me, I understand.

I am thinking, this is not considered a relevant thread---I am also thinking here I am using an angle grinder, an old 20 dollar drill press a welder I got cheap, and had to learn to use, and what hand tools I have on hand. I am almost there.