4. Weren't the puffs of smoke that were seen, as the collapse of each WTC tower starts, evidence of controlled demolition explosions?

No. As stated in Section 6.14.4 of NIST NCSTAR 1, the falling mass of the building compressed the air ahead of it—much like the action of a piston—forcing smoke and debris out the windows as the stories below failed sequentially.

These puffs were observed at many locations as the towers collapsed. In all cases, they had the appearance of jets of gas being pushed from the building through windows or between columns on the mechanical floors. Such jets are expected since the air inside the building is compressed as the tower falls and must flow somewhere as the pressure builds. It is significant that similar “puffs” were observed numerous times on the fire floors in both towers prior to their collapses, perhaps due to falling walls or portions of a floor.  Puffs from WTC 1 were even observed when WTC 2 was struck by the aircraft. These observations confirm that even minor overpressures were transmitted through the towers and forced smoke and debris from the building.

5. Why were two distinct spikes—one for each tower—seen in seismic records before the towers collapsed? Isn't this indicative of an explosion

11. Why do some photographs show a yellow stream of molten metal pouring down the side of WTC2 that NIST claims was aluminum from the crashed plane although aluminum burns with a white glow?

NIST reported (NCSTAR 1-5A) that just before 9:52 a.m., a bright spot appeared at the top of a window on the 80th floor of WTC 2, four windows removed from the east edge on the north face, followed by the flow of a glowing liquid. This flow lasted approximately four seconds before subsiding. Many such liquid flows were observed from near this location in the seven minutes leading up to the collapse of this tower. There is no evidence of similar molten liquid pouring out from another location in WTC 2 or from anywhere within WTC 1.  

Photographs, and NIST simulations of the aircraft impact, show large piles of debris in the 80th and 81st floors of WTC 2 near the site where the glowing liquid eventually appeared. Much of this debris came from the aircraft itself and from the office furnishings that the aircraft pushed forward as it tunneled to this far end of the building. Large fires developed on these piles shortly after the aircraft impact and continued to burn in the area until the tower collapsed.  

NIST concluded that the source of the molten material was aluminum alloys from the aircraft, since these are known to melt between 475 degrees Celsius and 640 degrees Celsius (depending on the particular alloy), well below the expected temperatures (about 1,000 degrees Celsius) in the vicinity of the fires. Aluminum is not expected to ignite at normal fire temperatures and there is no visual indication that the material flowing from the tower was burning.  

Pure liquid aluminum would be expected to appear silvery. However, the molten metal was very likely mixed with large amounts of hot, partially burned, solid organic materials (e.g., furniture, carpets, partitions and computers) which can display an orange glow, much like logs burning in a fireplace. The apparent color also would have been affected by slag formation on the surface.

Interestingly some of the steel members tested by FEMA exhibited corrosion consistent with thermite arson:

12. Did the NIST investigation look for evidence of the WTC towers being brought down by controlled demolition? Was the steel tested for explosives or thermite residues? The combination of thermite and sulfur (called thermate) "slices through steel like a hot knife through butter."

NIST did not test for the residue of these compounds in the steel.

The responses to questions number 2, 4, 5 and 11 demonstrate why NIST concluded that there were no explosives or controlled demolition involved in the collapses of the WTC towers.  

Furthermore, a very large quantity of thermite (a mixture of powdered or granular aluminum metal and powdered iron oxide that burns at extremely high temperatures when ignited) or another incendiary compound would have had to be placed on at least the number of columns damaged by the aircraft impact and weakened by the subsequent fires to bring down a tower. Thermite burns slowly relative to explosive materials and can require several minutes in contact with a massive steel section to heat it to a temperature that would result in substantial weakening. Separate from the WTC towers investigation, NIST researchers estimated that at least 0.13 pounds of thermite would be required to heat each pound of a steel section to approximately 700 degrees Celsius (the temperature at which steel weakens substantially). Therefore, while a thermite reaction can cut through large steel columns, many thousands of pounds of thermite would need to have been placed inconspicuously ahead of time, remotely ignited, and somehow held in direct contact with the surface of hundreds of massive structural components to weaken the building. This makes it an unlikely substance for achieving a controlled demolition.

Analysis of the WTC steel for the elements in thermite/thermate would not necessarily have been conclusive. The metal compounds also would have been present in the construction materials making up the WTC towers, and sulfur is present in the gypsum wallboard that was prevalent in the interior partitions.