Minecraft Java Edition Mods – Can Thaumcraft Bosses Spawn from Vanilla Spawners?

The solution I can think of is using MCP, which allows you to change the source code of Minecraft (including changing the animals). But if you can't do that, try using these files.

If you have 7zip, open up your minecraft.jar and paste the files inside the zip inside jar. Then delete the META-INF folder inside.

The Bounding Box Outline mod will show you nicely-shaded bounding boxes for all Structure Pieces placed in the world, including Nether Fortresses. It's currently available for 1.6.x and requires Minecraft Forge.

I've already got a Forge profile laying around, so it was a simple matter of dropping the mod in a fresh game directory along with the Skyblock 2.1 save, an edit to the level.dat to enable Creative, and lo and behold:

So yes, there are two Nether Fortress "ghosts" not far from the glowstone island.

The nearest corner of the one visible on the left is at approximately 76, 62, -63 (XYZ) and stretches to the North and a bit to the East from there, not including a hallway protruding to the West (the direction back toward the portal, but farther North than this corner).

The nearest corner of the one visible on the right is at approximately 94, 71, 73 and stretches East from there with a Southward and downward tendency.

You could go off those numbers and just grope around trying to make a blaze-spawnable area without the mod. If you want to use the mod though, it's quite easy to install starting from zero modding experience: download and use the automatic Forge installer which will create a new forge-enabled Profile, then drop the Bounding Box Outline mod's zipfile into the new .minecraft/mods/ folder that will be created after you run Forge once. Once in the game, turn the mod's visuals on by pressing F3+n (simultaneously) and the fortresses will show up bright as day.