Every 6 seconds is too quick a cycle, the squelch noise also sounds abnormal to me.
It is possible to replace certain sub assemblies, but the issue is how you go about diagnosing the issues; which is where it becomes tricky. It sounds like the the issues could be an Accumulator or Accumulator Pump (either the pump is supplying borderline acceptable pressure and needs to run too often to "top it off" or the Accumulator is leaking pressure), but it is also possible there is an internal leak in the master cylinder portion allowing pressure to bleed back into the return circuit, and/or a similar leak in the ABS Solenoid pack mounted directly to the master cylinder portion.
The reality is that you're better off replacing the entire assembly as a whole than trying to replace parts one at a time with this system. As for paying $3000? That's up to you, there are other options available to you that may make the repair a bit more affordable.
-Pay the dealership the money and have a 1 year warranty on the part and work done (that may be worth the high cost? It's up to you on that one...)
-Call the Parts Department and acquire the Part Number for the unit and then shop online.
(For example
BRAKE BOOSTER ASSY, W/MASTER CYLINDER. BRAKE MASTER CYLINDER (GRN21# for 2008 TOYOTA 4Runner. #4705035031 appears to be the correct unit for your vehicle) then have the dealership install it for you (they mark up the price of the part to closer to $3000 usually vs. the almost $1900 on the website.)
-Locate a used unit from a salvage yard for cheaper (there are inherent risks with this as you don't know the vehicle age, service history, ect. of the unit; but they are often fairly cheap.) and have the dealership install it.
-Live with it until the unit goes completely out?
Either way I recommend you have a Dealership do the repair or a shop that is very familiar with the Toyota system and has the appropriate scantool to bleed the system afterwards.