Right, first off I'll introduce myself as a new Audi A4 owner! *cheers*

The car in question is a 1997 Audi A4 Quattro 2.8L Petrol with 192bhp (a long time ago perhaps) and a 5 speed manual.

I got this saloon for £500 which isn't a lot, and there is reasons for that as I'm about to explain.
1) The battery isn't holding a charge very well (which might be the cause of the other problems??)
2) The ABS light is on - although at times does go off... loose connection?? or new pump needed? or is this related to the battery in any way?
3) The Rear LED brake light is always on... I don't know if its supposed to be or not? It DOES get brighter when braking but I didn't want to take the risk of it and unplugged it since it isn't required...
4) The passenger side front side light is always on... and the main beam comes on when you touch the brake peddle? (this happens when the lights are set to "off"
5) as such there is a warning on the screen on the dash to tell you a bulb is out...
6)the car pulls and is needing re-aligned
7) Finally, the engine doesnt run as nicely as expected and sometimes cuts out... more than likely battery related right?

The good parts of the car outweigh the bad in my opinion (although my eyes may be blurred by the fact I love the car...)
It has a 6 CD changer in the boot and some decent audi equipment...
it has a 0-60 in less than 7 seconds... perhaps faster, Im not sure but its fast!
its 4wd! and as such is insanely nice to drive...
the v6 means cruising around in 5th gear at any speed is possible as its so smooth!
The gearbox and clutch were changed completely in 2009 (i have a full history for this car) and costs £3850 to do this!
I have done the basics so far: new spark plugs, oil change, oil filter, fuel filter, pollen filter, air filter, brake discs, pads and one new tyre

So overall... I want to fix all the problems and use this car as I currently do... it has 3 months left on its MOT and so I need to be quick in solving the above problems.

Any help would be appreciated... I'm an engineer for a very well known company so I know how to turn a spanner and how everything works but I'm not a mechanic and I don't have experience with problems like these so I would be forever in your debt if you helped me

Some pictures:

 

That's really a nice-looking A4, especially for the low cost. The symtoms that you describe concerning the brakes and some lights are definately not correct. Sometimes the culprit is an incorrectly installed bulb in the tail lamp assemblies. People will install a dual-filiment bulb where a single filiment is intended, or vice-versa, with abnormal things resulting. The usual advice with these, or any Audi/VW vehicles, is to obtain a scan tool, such as the popular VCDS software for your computer and diagnostic cable. A common OBDll scan tool may access only the Engine Control Unit, and not the other modules on the data bus. By the way, it seems that being an Engineer often means buying a challenging, but technically interesting car, and the enjoyment of solving its faults.

 

Im interested in the fact that your headlight is on as well as your brake light AND your brake light gets brighter as you press the pedal. All that, I believe is supposed to happen when you have the lights on. Occam's razor says that you just have 1 brake light out (the one that isn't on) and one headlight out (the one that isn't on) plus a bad fuse or two... Now my theory goes straight out the window if your other head/brake light come on as they should during normal driving...
My inclination as a real general sense would be to do two things, first do as turbo said and get a scan tool. VCDS/Vag-Com is light years better than a general one, but also significantly more expensive. Mine was $30 and reads CEL's fine but doesn't do anything else, and I'm fairly content.
I would also get your battery tested and possibly get a new one. It's possible the battery is fine and you have a bad alternator, but a brand new battery never hurts... Especially if you don't know the age of the old one.
Lastly, if you can afford it, consider two new headlights and brake lights. Like the battery, a new set is never a bad thing on a car you're not sure the age of (the lights obviously).
Take this all with a grain of salt because my tendency is to lean towards the replace-rather-than-test methods because I like having new things and not having to worry about whether I tested it correctly and having it still be a fault when I'm trying to diagnose an issue, only to come back a month later and find I just didn't test the part correctly.

In any event, good luck!