1) you didn't say this. You merely stated that the warning light was on. This implied that you a)hadn't checked the pads, b) didn't have the wherewithal to check them. If you had stated "warning light is on, I've checked them and they still have 4-5mm on" you would have got a different response.
2) Changing the brake pads yourself could not possibly have affected the warranty issue with the gearbox. Trading Standards would have had a field day as they are totally unrelated.
3) Only you can be the judge. As per point 1, your initial post didn't lend itself to believing you had vast amounts of experience.
4)You do not have to have the car serviced and maintained by the supplying or manufacturing dealer. Googling European Block Exemption Regulation (bit of a mouthful I know) yields this from wiki:
"Prior to 2003 automobile owners in the EU region risk nullifying their vehicle warranty when the vehicles were serviced or repaired in workshops not belonging to the vehicle manufacturer or its dealers. This barrier was broken in October 2003, when the European Commission (EC) passed a law allowing vehicle owners the freedom of having their servicing and repairs done at their chosen workshop.
According to the UK Department of Business Education & Skills, the empowerment created by this law provides competition in the automobile industry as vehicle owners now have the opportunity to repair and service their vehicle at alternative workshops to the automobile manufacturers. BER provides automobile users the flexibility and benefit to reduce the amount spent on servicing, thereby providing consumers more choice and better value for money."
http://en.wikipedia.org/wiki/Block_Exemption_Regulation_(EU)
Essentially, you have the freedom to have your vehicle serviced and repaired where you see fit without affecting your warranty, as long as the garage carrying out the works demonstrate oem quality parts and that they are competent. In the UK, being VAT registered is usually seen that the garage is bona fide, and I know of two instances where this has been accepted (one vauxhall, and one renault)
In this section, you mention your limitations, which would imply again that you do not feel totally comfortable with doing the job yourself, which is at odds to your point 3.
Finally, point 5 (although you numbered it 4 again), at least we agree on something about kwik ****.
good luck.