I personally see no problem with the MSD coils, though you will get a wide variety of opinions on that. I think most put them on there with the expectation of some kind of noticeable performance gain and thats not really where their focus is at. Those are more powerful coil pack 48k Volts vs. Stock 38k I believe. Which will give you much better spark at the plugs and might help with fuel economy as well because of the better spark.
The 180* thermostat is fine. 160 would be too low, but 180 is a much better choice. The only thing I would have done differently is run MSD plug wires. Simply because they are much lower resistance than stock, lower resistance than any other after market wires Ive seen and would let you take full advantage of the coil packs. Ive never used the NGK plugs so I cannot speak to those directly.
With regards to doing the tune up, yes you will need to disconnect the upper motor mounts on the engine side so you can tilt the motor forward, but I have never heard of having to jack up the bottom end to do the work or to tilt if forward. Unless the 04's do something differently with the mounts, I dont see that being necessary.
