Pre-requisites:
-2 universal (metric) MC bench bleed kits (for ABS setup) or 3 kits (non ABS setup), ~$4.99 each in Autozone (special order, p/n 13999)
-at least 1 big (32oz) bottle of brake fluid, the more the merrier
-3/8'' dr ratchet with extensions and 10 & 12mm socket
-3/8''or 1/4'' torque wrench recommended
-pliers
-2 tooth brushes or nylon brushes, some water maybe needed
-grease (e.g. Permatex Ultra or Ceramic Extreme)
-big Philips screw driver or other means of pushing the MC piston in (I used a highlight marker)
-11mm flare nut wrench
-all you need for regular brake bleeding/flushing
-lots of time, you will be flushing brake fluid at all 4 corners once done with replacement
As you can see the access to Master Cylinder on 1mz-fe is a little cramped hehe
First raise the rear end of car and put it on stands. doesn't have to be high, just enough for tires to get off ground. It will help keeping the MC fluid at level.
Remove the strut brace (if any), usually 14 or 15mm socket with extension does the trick.
Torque is 29ft-lbs on my Monroe mounts, OEM original was 59ft-lbs, but who knows maybe that WAS the reason old mounts (KYB on gen4) were failing and having stripped studs?
Unhook the intake air box's top portion only, 2 metal clips on driver side, unhook a springed hook thing from cable on engine side also.
Disconnect the MAF connector (and wire clip below it – use pliers on it after lifting the whole thing up, easier to access this way)
Hoses to disconnect:
-Intake from throttle body (10mm socket to loosen the clamp)
-Unplug PCV hose (use pliers on clamp to move it away) from the engine's front valve cover.
-Unplug EVAP hose on both ends, one to air box cover, other end on VSV (you will need working space for MC removal).
-Unplug tiny vacuum hose from air box cover on engine side.
Lift the air box cover up along with resonator, intake hose and PCV hose (wiggle it out from the surrounding cables)
After removal it should look like this:
working area:
I also discovered that my EVAP hose is cracked on both ends, so it might be a good time to replace it as well.
Remove old MC cap (on car) and filter and suck out all the brake fluid from there that you can.
You can use either a Turkey Baster or a hand Vacuum pump.
Cover the MC filler opening with plastic wrap and install the rubber cap on it securely. Put some shop towels below the MC and around, there will be fluid spill soon.
Undo both brake lines (11mm flare nut wrench) from MC assembly (ABS setup in picture).
You can clean the ends of brake lines with a toothbrush and water if needed, then wrap both brake line fitting in plastic wrap to avoid any dirt getting into them.
Disconnect the Brake Fluid sensor connector from the MC assembly.
Remove both nuts (12mm) holding the MC assembly to the booster. Passenger side nuts also holds down the 3-way brake line connector (or 2-way on ABS & TRACtion control setups), slide it off before you start removing the MC assembly!
Wiggle the MC out from booster studs, brake lines and remove the brake sensor wire from plastic clip. Keep it level, it will leak fluid from ports if you don't. Here is how mine looked like, utter piece of garbage. The rear end of piston was rusty!
Remove old gasket and grease from booster. Mine was a little rusty around the pushrod o-ring. Use any tools for cleaning you like, just keep in mind that there is a rubber o-ring, so don't use any metal wire brushes or brake cleaners.
This is how old gasket looked like:
Booster opening BEFORE cleaning:
Once clean, put new grease on the push rod and o-ring. I also put some grease on edge of circular indentation to help keep the gasket sealing better. Inner walls of that indentation are rusted on my booster and I wasn't able to clean it off without using wire brushes and brake cleaner (didn't have new o-ring for push rod and old one was still good).
AFTER cleaning and re-greasing (new gasket is not in place yet)
Bench bleed the new MC assembly.
Keep the new MC assembly level. I used a temporary stand made form the box it came in.
MC bench bleeding kit (universal metric), single kit in picture, you will need 2 or 3 of them as each one contains only 1 matching port fitting.
Bench bleeding in action (early progress):
Bench bleed done, no more air:
In summary, you need to use plastic M10x1.00 flare fittings in the brake line ports (hand tight is fine), attach the hoses to them securely (all the way in), install the one way valves on other ends of hoses and clip them to filler opening. Worth mentioning is that you should make the hoses output ends sit above the fluid level in reservoir, otherwise you will be sending air bubbles into the fluid in MC reservoir (defeats the purpose).
Use either #2 Philips screw driver or any other tool being able to push the piston in (I used a highlight marker for better grip) to push the piston slowly in and slowly out as you bleed the MC.
Keep the fluid level in reservoir at MAX often, don't let it drop below MIN. Eventually both chambers will fill in with fluid and at some point the air will stop coming out from hoses. Once there is no more air coming out (just fluid) and both chambers are full of fluid, it's good for install.
NOTE: the secondary chamber pushes fluid out later than the primary chamber, so don't be surprised if one of hoses, coming from port furthest to booster end, doesn't squirt the fluid right after pressing on the piston.
Now, unclip bleeding hoses from filler opening and clip them together. Put plastic wrap over the filler opening and install the cap tightly on it – It will prevent fluid from spilling once you remove the bleeding port fittings later!
Carefully bring the bench bled MC assembly over (with all bleeding plugs and hoses still attached) the booster and visualize how you insert it into place. Remember that brake lines must go the same way, they do not allow for much play (metal), so don't force things if something doesn't fit at once. Back off and try again.
You may need to align the brake lines BEFORE putting the MC onto studs.
Once MC is hanging on studs, install the 2- or 3-way connector on passenger side stud. install the MC to booster nuts (9ft-lbs), but don't tighten them yet! First check if the brake fluid level sensor wire is i=clipped in place behind the MC assembly. Once you tighten it, you may not be able to slide it back in place over there!
I was able to use my 3/8'' torque wrench with 12mm socket and extension on the nuts with no problems. It's tight on driver side (one ratchet-click distance), but doable.
I am tightening those nuts in picture below, note how ports are still carrying bleeding fittings and cap is air tight (plastic wrap under it).
Then unscrew the bleeding port fitting one by one and reinstall loosely the brake lines (again do it one by one to avoid major spills!!!). Then tighten the brake lines flare nuts (11ft-lbs).
Eventually on the end you will have this
Install the rest of stuff in reverse order.
NOTE: it might be a good time to clean the throttle body and IAC hole before you put the intake stuff all together
Remove the plastic wrap from under the MC cap and start flushing the brake fluid until you see no bubbles. Refill to MAX lines (or a little over) after each 100mL was flushed out.
Correct bleeding order is RR, RL, FR, FL.
Flush at least 250mL from rear brakes each and/or until no more bubbles.
Flush at least 100mL from front brakes each and/or until no more bubbles.
Good luck!
Disclaimer:
If you screw up something or hurt yourself…that’s your fault. Neither myself nor TN are responsible for any injury, damage, or even death caused by this DIY
DIY Master Cylinder replacement (1mz-fe / others similar) *PICS*
Piece of Crap
I hope I can get the sticky up to version 3.0 by the end of spring break! I'm about 11.293892% done. 
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