I will do my best to address your concerns.
I would recommend that you hold off with any updates until you are clean. Let's see how things progress after removing those Trojans in the mwav log.
Though I can understand your inital suspicion, my guess would be this is nothing more sinister then a coincidental hardware failure.
You may find these links enlighting. Castlecops McAfee
Those .js files are JScript While that does not mean that they are malware, they can be. You may want to Google those and if you find they are bad, remove them. If you are denied access, they may be r