The problems you describe are quite common to older homes that have cast iron soil pipes and galvanized iron water pipes, especially if the water supply has been turned off for an extended period of time.
You toilet is flushing ok because it is connected directly to the 3" cast iron waste pipes. While cast iron pipe does rust, the rust on that type of pipe is generally little more than a reddish film on the pipe wall and it causes no serious problems, however, in most instances they only used cast iron pipe to make the primary runs of 2" or greater diameter. The smaller runs of 1-1/4" or 1-1/2" diameter were generally made of copper pipe, brass pipe, or in most cases Galvanized iron pipe. When you have copper or brass pipe it is very unlikely that you would have any major corrosion that would obstruct the pipe, but those types of pipe commonly corrode through the pipe walls on the underside of the pipe causing a lot of leaks. When the smaller waste arms were constructed of galvanized iron pipe they often used cast iron reducing Tee's that had a threaded side opening to permit directly screwing a threaded galvanized pipe into the cast iron. In many cses they then used galvanized pressure type 90's and Tee fittings which makes snaking the pipe nearly impossible.
In most instances you will find the cast iron soil pipe is still perfectly servicable and the galvanized iron pipe is only used on the short waste arm runs from the vent stack to a tub, sink or lavatory drain. You can cut the galvanized pipe about 1/2" from the hub of the cast iron fitting, then using a hammer and small cold chisel you can pry the remaining threaded portion of the galvanized iron pipe out of the cast iron threaded hub. Next clean the cast iron hub threads with a wire brush, then you can then apply a liberal coating of pipe dope on the threads of a PVC male thread adapter and screw it into the cast iron hub. From that point you can replace the short waste arm section from the stack to the sink or tub trap with PVC pipe.
You stated that the the water supply is also galvanized iron pipe and you are getting discolored water. The first step here would be to have your water quality tested.
In most instances if the water is comming from a treated municipal water supply the discoloration will pose no health threat and should diminish in a short time by flushing the system, however, in some instances when the water supply has been turned off for an extended period of time and there is the possiblity that air got into the lines or if the water is coming from an untreated home well system there is a strong possibility of microbiological action having taken place and the water could present a potential health threat. (Most municipal water suppliers have facilities to conduct water quality tests for a very reasonable fee, contact your local health Dept. for information on how to get tests in your area.)
Whenever we encounter galvanized iron water supply pipes that are severely corroded the only practical solution is to replace the pipe with copper, CPVC or PEX tubing.