Because you appear to have two issues (morning noise/alarm and leaking master cylinder) I think you have a few options:
First of all, here's what we're dealing with.
In this diagram, you can purchase the whole assembly or a few sub assemblies, or some individual parts.
- #1 (part #47050-35010) is the entire master cylinder/ABS module + booster motor/pump/accumulator. Available new for ~$2100
- #2 (part #47025-35010) is the master cylinder/ABS module (without the booster motor/pump/accumulator). Available new for ~$1200.
- #12 (part #47070-60010) is the booster motor/pump/accumulator. Available new for ~$800.
You can probably find a used assembly (equivalent to #1 above) for ~$500 or maybe even less. The trouble is it might have the same issue as yours...there's no way to know until you install it.
You could also just rebuild the master cylinder piston with the overhaul kit from Toyota ($65, part #04493-35340) but that will only solve your master cylinder leak...not the morning noise/alarm.
You could buy a new master cylinder/ABS module assembly (#2 above) for ~$1200 and that should solve both your leak and the morning noise/alarm. If you want to go with new parts, but are budget constrained, that may be a good option, but you'll have to do some disassembly and transfer your booster motor/pump/accumulator over. Also, some people end up having one or more of those parts fail eventually too, at which point you'd have to replace those as well, costing more money.
Or you could just bit the bullet and replace the whole assembly with a new one, and probably be good to go for another ~15 years, 180k miles. That's the option I chose to go with because it essentially refreshed all of the components to new, and I have peace of mind knowing that I haven't introduced some failure point by taking the system appart.
Good luck with whichever way you chose to go!