2006 Vauxhall Vectra several electrical faults!!

Hi, im hoping someone can help me..

I have a Vauxhall Vectra sri 2.2 direct, 2006 plate. Last year the gearbox went so i parked it up for about 6 months, until i managed to buy a second hand gearbox, and fitted it myself. I also replaced the clutch and clutch release bearing. When I started the car, battery wouldn't hold its charge, so i took it to a local garage who advised an alternator replacement. I bought a 2nd hand alternator off ebay, (which cost just £35) and ever since, all of my electrics have problems. I shall do my best to try and describe them, i just hope someone out there somewhere knows what the problem it!!
When you start the car, then try and put the headlights on, the wont come on. However, if you leave the dial turned on, then disconnect the batter and start the car again, they will come on, but you cant then turn them off with the dial. The central locking doesn't work. The boot wont open, again if you disconnect the battery and reconnect, the boot will then open. The hazard lights work, but the indicators don't. And the brake and reverse lights don't always work. The sidelights and full beam do work. And when the headlights do come on, they flicker constantly. I have had the car put on diagnostics at another garage, who said "parts of the ECU aren't communicating with each other" Ive been searching online and forums and some say it could be the BCM board or CIM board.. Also I'm thinking moisture could of corroded something with it being sat for so long. Or maybe I bought a dodgy alternator which maybe doesn't work properly or could it be possible that its fried the ecu? If anyone has any idea on what could be the matter it would be so much appreciated. Thankyou!!!