I've been looking for a new guitar for a while. The specs I've been looking for are; Mahogany body,Licensed Floyd Rose, Neck Thru, with Ebony Fretboard. I can't spend for then $600 and the only guitar I found with these specs are the Esp Ltd F-2e http://www.musiciansfriend.com/product/ESP-LTD-F2E-Electric-Guitar?sku=515734
The problem with that guitar is that its backordered till 3-28 on every guitar website. So if anyone has suggestion for a guitar with these specs please let me know.
I think that ESP'll probably be the best you'll find for that money. If you find any other guitars with those specs they'll probably have the ****test floyd rose ever.
The Dean Vendetta 4.0 is mahogany, neck-thru, has a floyd rose and comes equipped with Dimarzio Super Distortion Humbuckers, and an ebony fret board and is around $600.00
Also I believe it has a quilt maple top
For some reason i can't find one on the music web sites
Out here you've gotta know where your towel is!
I think your choices literally are that or a custom built guitar. There really isn't any other guitar that fits all of those specs (there isn't even a more expensive version of that guitar with those specs because the higher end versions are either Swamp Ash or Alder).

When you are that specific, you really are limiting your choices. There are other decently good mahogany bodied guitars with locking tremolos, if you will budge on the fretboard and the neck thru. Ibanez S series are Mahogany and a couple of the models have set necks and I think a couple of them might be in your price range. You may be able to find a used Schecter Hellraiser FR in your price range, but that is also set neck and Rosewood fingerboard.

Also, it is listed as being in stock at musician's friend. That might be a typo, because I was pretty sure it wasn't due out until March.