A couple more things - if you got the blink example to compile but it doesn't perform as expected, can you check the compiled hex filesize vs. the result from the Arduino IDE? Often, a successful compilation but strange behavior at runtime is due to compiler and linker optimization settings that differ from the defaults.
Also, I didn't realize you mentioned debugging with the simulator in your first post - that's a different beast than debugging on-chip, and we've had trouble getting consistent results (plus, it's sloooow). Not sure if you have a programming tool, but using DEBUGWIRE with a Jtag or AVR Dragon has been a better experience.
If you're looking to try again and would like instructions to cross-reference with Jaycon's tutorial, we've updated our AVR Studio 5 tutorial for using Arduino with Atmel Studio 6. It can't account for every variation in people's setups, but a good number of users have found the previous version helpful. Let us know if you make progress and we'll share any other insights we have!