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Almost certainly what you have done is cause the master cylinder to develop an internal leak, probably by over-enthusiastic bleeding. I know, because I have done it myself before I learned NEVER to pump the pedal when bleeding further than it travels in normal use. This runs the seals over unused sections of the bore, which may be dirty or corroded. Once the rubber seals have been damaged the internal leakage means the two circuits may have different pressures.
You need a new MC. The light will probably cancel itself (dismantling not recommended, and usually unnecessary). Don't ignore this - brakes are a matter of life and death, and with only half the system working you have already lost one of your two lives.