To my knowledge, command blocks can not run in unloaded chunks. This means that they must be in perpetual world spawn chunks, or they must be inside your loaded chunks when you are within range. This could help you narrow down which area it’s coming from.
If they happen to be in the world spawn chunks, you could move the world spawn somewhere far away to stop them from loading, then continue your search.
You could write down your current coordinate when you notice the problem, then approach the zone from an entirely different direction, noting your coordinates when it happens. Knowing your chunk view distance should allow you a crude way to triangulate the possible location of the command blocks.
Then, you could attempt to use World Edit,or the native Minecraft fill command, to replace any command blocks with another block across large regions.
If you put your world into a server, enable command blocks, you should see the commands in the console and get a log file of what the command are. You can then use nbtexplorer to try to locate the command, as described here: I've lost a command block, how can I find it?
The other thing I can think of is trying the spigot server plugins AntiRedstoneClock and Redstone Clock Preventer, though I am not completely sure these would do what you’re looking for.