Ok, so I'm starting a brand new file. 
Ok, I give up on this, somehow it is telling me everything, including my connections, are corrupted. :'(
Maybe, maybe not. You can get lots of clearance errors when doing things like putting drill holes into manually added copper rectangles, etc.
On my light analyzer board, I wound up doing the DRC then putting in the thermal vias around the high power connectors.
Would it be a horrible idea if I just sent in the order despite some conflicts, who knows they may be able to produce it?
It basically looks OK. One thing is the No Vector Font errors on that “Scaru” text. Text in the signal layers needs to be in a vector font. Select the text and change the type to VECTOR. Also, there are two SCARUS on top of each other on the blue layer. Delete one of them. Or put the text on the silk screens, not in etch.
Seeds design rule file says 12 mil min drill size, their web site says .3mm (11.8 mil). That’s causing the drill size errors.
Other than those, it looks like it might fly. The clearance and overlap errors seem to be due to the drilling into polygons, etc.
Ok, I fixed a few things, here the gerber file is.
http://dl.dropbox.com/u/84514277/Completed%204%20xml.zip
I think I'm just going to order it and see how it comes out.
Not bad for a first run with Eagle. It’s been a long time (and a lot of versions) since I tinkered with it, but I don’t remember it being the most intuitive program 
Comments:
1 ) The text on the top silk-screen is off the board - it will be cut off
2 ) Not sure if it was your intent or not, but the 4 emitters are not centered on the PCB - they’re shifted to the right quite a bit
3 ) No via’s for the thermal pads? Or maybe they’re in the design and you just didn’t export/create the NC-Drill file?
And change the name of the E$5 net to something meaningful…
I would also do the wiring to the left hand leds the same as the right hand ones (connections to the LED power pins) Run the connections vertically and don’t come into the LEDs via those little nubs. That tiny gap between the power etches and the LED pads is not a good thing.
Also, bring the etch into that E$5 pad in at an angle. It is currently forming a very acute angle with the hexagonal pad… that is known as an acid trap. Also, if you can, try to avoid right angle turns in an etch. Not as important these days, but it is good form.
1. I don't care. :P
2. Again, happy to hear that they exist at all.
3. Hmm... They are in my eagle design, but I guess they didn't get exported. I will try to figure it out.
1) it’s trivial to move the text
2) easy to move the whole or section of the layout (via Move Group command)
3) yep, it looks like the drill file didn’t get processed
Ok, so would this contain the drill holes? I think I must have forgot a section.
http://dl.dropbox.com/u/84514277/Completed%204%20xml%20v2.zip
@Texaspyro, how exactly do you do it? The only thing I could figure out was how to move the whole contact pad.
Yep, there you go. The .TXT file is the Excellon NC Drill
Ok, I made a few more changes.
http://dl.dropbox.com/u/84514277/Completed%204%20xml%20V3.zip
I think this may be ready to be ordered. :D
Ship it.
Sweet, BTW can traces intersect? I'm asking because I was thinking about making a monster 7135 board, but I'm not sure how I could do it without the traces intersecting.
I’m not sure what you mean by intersect, to be honest. That board you just posted would fail miserably. You’ve got pin 2 and pin 3 tied together (at a minimum, I stopped looking after seeing that). That’s why you have two layers and vias. When you need one net to cross over another net, you drop a via and continue the trace on the opposite layer - thus running “Under” or “Over” the other net.
PPtk
Place all chips in a grid, then use vertical traces to connect all chips in each column.
Add 3 horizontal traces to connect all the vertical traces.
And remember a fan to get rid of the heat 
It is a long time ago I last did a layout in Eagle.
As in can two vias go across eachother? I'm thinking not...
Ok, I'll arrange them that way. Thanks.
You use the GROUP command/icon to define a group (either a rectangle or a polygon). Then select MOVE GROUP to move everything within the group.
To do a rectangle group you click on one corner and drag the mouse while the button is down.
Texas, am I correct in thinking that the wires going from one place to another cannot cross each other?
Edit: they are called traces correct?