1. For making blocks unbreakable, Thaumcraft offers warding through its wand system. You have to make a wand focus for warding, then you can apply it to most blocks and make them unbreakable, even by other players.
I'm sure there are others, but I don't know enough mods to give you other options. Though depending on your goal, there may be other ways to get what you want. If it's a matter of unbreakable from explosions, from wither, etc., there are mods that offer wither-proof or otherwise highly-durable blocks. Draconic Evolution has some wither-proof blocks, iirc.
2. AE2 makes it very easy to auto-craft items of all kinds, though it takes some work on the front-end:
A) You'll need your ME system set up (storage drives, controller, power, cables, etc.
B) You'll need to figure out what processes are involved in your item's creation. If it's all done in a crafting table, that's the easiest.
C) You'll need to add the auto-crafting components to your system. The first is a processor, which requires crafting storage and co-processing units. I don't remember offhand exactly what the storage does in the process, but co-processors lets your system multi-task, or run multiple steps at once. This is a multi-block structure that uses both of these blocks together, either in a square or a rectangle. The second is your interface/molecular assembler portion. The molecular assembler can be used by any interface touching it. It requires power but no channel, whereas the interface requires a channel. You can surround the interface with 5 assemblers if you want, so it can run multiple jobs at once to speed things up. You can also combine multiple interfaces and assemblers in a larger block in a checkerboard pattern--though this can be tricky given how finicky AE2 can be in managing its channels.
D) You'll need to use an ME Pattern Terminal to create your crafting patterns. This is also where you'll set your Processing Patterns, if applicable (see step five). These will go in the interfaces for use in the assemblers. Skip to step six if you don't need external machines (e.g. Thermal Expansion, EnderIO, etc.).
E) If your item requires steps that use machines rather than a simple crafting grid, then you'll need to use Processing Patterns to tell your ME system that it needs to send items to X location and wait for the results to come back in. This is usually done with Export/Import buses, but there are other ways of doing it too. Once those machines are set up with their AE2 export/import bits and you have your processing patterns in place, go back to your ME System.
F) You should be all set to run your item through the auto-crafting process. Find your item in your ME system, and if there is not one of those items currently stored, instead of showing a number, it will say, "Craft." Click that, and you'll be given a screen that asks for a number. Set the number, and it will show you a summary of the items it needs and whether everything is there, in addition to giving you the option to select which processor you want to use (some people make a bunch of tiny ones and a couple big ones for big jobs so they can run a lot of different kinds of crafting requests). Assuming you have everything set up, just give it the go-ahead and wait. Once the assemblers/machines have all done their thing, the item will pop up in your system, ready to be taken out and used.
For other types of crafting (thaumic essences, liquids, etc.), you'll need specific mods installed for support. Infinity Evolved has several add-ons for AE2 that enable it to auto-craft things from Thaumcraft, for example. Just having Thaumcraft and AE2 won't do it, as AE2 doesn't have the import/export buses for essences.
3. Can't help you there.
