Changing a signal's DC offset before amplifiter and ADC
As the output voltage is not at the correct DC level, but the DC bias is correct, change the amplifier. There is lots of other good advide here, particularly @ChrisR decoupling comments. Another point to note is the the virtual earth connections (ive Opamp inputs) are very sensitive to capacative pickup, so ensure that they are routed close to the amp and do not do near potentially noisy signals.