The various things that you mentioned have no common electrical distribution or grounding, which makes a wiring harness issue more likely. However, I'd first start by doing a static and load test on the battery, if you have not done so already. If the charging system tests ok, then try evaluating one circuit to see what's going on with that. The driver side power window switch probably has the shortest and simplest run to the fuse box, if it comes to chasing wires, so that one might be a good first choice. Disconnect the wires to that P/W switch, test for power and ground, and then continue the testing based on those results.