I have an 03/2002 R50 5 speed manual, second hand with 160000km now at 176000km in 3 months. Replaced the PS pump Aus $1000.00, Engine mounts (1 was about to fail so I replaced 3 of the 4) Parts Aus $350.00 approx., Replaced the OLD style fuel filter (you have to replace the whole unit) Aus $400.00 and a new fuel pump Aus $375.00 ! Am I concerned ? no, its a 12 yr old car with poor prior maintenance. Previous owner used the wrong PS fluid (will damage the pump, never replaced a seized PS cooling fan (lazy), failed engine mount, normal wear and tear. Fuel pump and filter, luck of the draw ! At the present time, its running fine. Gearbox is Midlands, shifts without issue and cant fault it but I also don't flog the car to death and don't ride the clutch. Labour on repairs is done by myself so that cuts down the cost. Looking at dropping the sub-frame in the future to replace ball joints and bushing, more a preventative maintenance than current need.
For any second hand car you should expect problems without an exact maintenance record (I'm recording mine) and as its a BMW, you expect to pay for the brand name so if your capable of doing your own labour you can save money. One thing to consider with issues like gearbox failure, forums will only ever tell you about ppls issues when things go wrong, what are the actual statistics of all the Midlands gearboxes that have failed world wide and how were they driven ? how many never had an issue ? A rebuilt Midlands gearbox on EBay Australia in Sydney is offered and almost Aus $3000.00 supplied and not fitted so its not a cheap gearbox. Remember its a 12 yr old car, thing will wear and need to be replaced. Preventative maintenance is your best bet, regular oil changes and filters etc. Don't drive it like you stole it but do drive it spiritedly. Look after it and enjoy it and it will probably serve you well. There are some good websites and Youtube Videos for maintenance etc, Mod Mini on Youtube has some very informative videos and a good website is BillsWebSpace and Pelican also have some good repair/maintenance articles.
With some decent tools, they are not that hard to work on and maintain, also recommend the Bentley manual for ref and repairs.