The Merlin 1D engines can restart up to four times, they use the pyrophoric mixture of TEA-TEB (Triethylaluminum-Triethylborane) to ignite the engines. My question is where is this stored in the engine so that it can be released several times to restart the engine?
The specifics of the Merlin 1D engine layout (and the detailed schematics of the Falcon 9) are proprietary, so there unfortunately isn't an official diagram that one can point to in order to answer this question. For what it's worth, however, it does seem that the TEA-TEB is being stored in the fuselage for each restartable stage (in the same section of the Falcon 9 as the LOX tanks), not in the engines. This placement would be consistent with the what one of NASA's Safety and Mission Assurance reports says about the second stage restart problem on Flight 6 of the Falcon 9 (back in 2013):
Frozen fluid lines for the Merlin 1D Vacuum engine's hypergolic igniter fuid (triethylaluminum-triethylborane, or TEA-TEB) were responsible for the failed second stage restart. The lines froze when they were exposed to liquid oxygen boil off. Designers added insulation to the lines and reoriented systems to prevent GOX impingement on the lines in preparation for the next Falcon 9 launch with SES 8.
For the TEA-TEB lines to have frozen from exposure to LOX boiloff, it's likely that they were in proximity to the GOX vent. Since the LOX tanks and the GOX vent are both located in the fuselage, one would presume the tanks from which the TEA-TEB lines are originating would have to be in the fuselage as well. Given that the combustion chamber (the end destination for the TEA-TEB, and where the LOX and TEA-TEB mix to cause ignition) is in the engines, if the TEA-TEB was being stored in the engine section there wouldn't really be a reason to run lines near the GOX vents.
Edit: The Falcon 9 user guide states that there are 2 TEA-TEB tanks for redundancy; given the failure mode of Flight 6, it sounds like they're located very near each other.
This all seems to be supported by an (unofficial!) system schematic of the Falcon 9 that enthusiasts have put together based on publicly available data, tours of SpaceX, etc., which shows the TEA-TEB tanks as being located in the fuselage for each stage.