First of all, those looms are in a horrendous state, and won't be helping anything. Didn't you receive new ones with your facelift lights? Those horrid scotchloks need to go ASAP (those red plastic connectors) they are terrible things at the best of times, but you can see the wires in them are corroded.
When you say "When I plug them in they light up wrong; The indicators light up the reverse lights", do you mean that when you turn the indicators on, the reverse lights come on as the reverse lights normally would, or are the reverse lights flashing?
Always start with the easy stuff - are you sure you have the bulb holders in the correct place on the lights? IE, are the looms mixed up or installed backwards?