The trojan is related to the mining that is still in-wallet in the 0.9.x code base. We are working on an 0.10.x "core" version of OFF soon which will eliminate the false positives for this wallet.

Also, the I/O error will be solved by the next release as well--we're cutting off the old peers who don't upgrade past this version, thus that bad peer (with an incompatible database we believe) will cease to bounce people. In the meantime, use the zipped blockchain to get around that.