The recall for the VANOS was for the oil pressure line leaking, not really anything caused by the VANOS, or anything other than a poorly designed oil line. It also only affected cars produced up until late November '05. The big problem with the VANOS is people not changing the oil regularly, or using the wrong oil. You HAVE to use Castrol 10W60, period. Period, period, period. Some people use LiquiMoly, I personally am not a fan, as I've torn down engines using LM, and the wear is noticeably different (read: worse). Castrol 10W60 isn't cheap, either. BUT, it's a lot cheaper than a motor, or replacing VANOS units.
As far as the SMG issues, I haven't seen a whole lot of them on M5's. Most of the issues I've seen firsthand have been on the older E46 M3's. I have heard of issues with the E60's, and of customers having hydraulics, gearbox, clutch and flywheel replaced MULTIPLE times...but I haven't experienced it firsthand. I know that Jerry at Eurocharged holds a few Texas Mile records with his, and as long as I've known him I haven't seen it have any issues. I haven't talked to him in a few months, so it's possible that he's developed an issue since - but he uses his car as a test platform for Eurocharged's tunes and products, and beats the ever-loving shit out of it, and AFAIK hasn't had an issue.
I'm personally not a big BMW fan, they just don't have the reliability of Mercedes or Porsche, and repair cost on BMW's tends to be a lot more expensive. The common things that fail on Mercedes are valve cover gaskets and rear main seals, for the most part (exception of the balance shaft issue on the 272); stuff that commonly fails on BMW's are high pressure fuel pumps (e90), the entire K-can system (anything with the RDC module in the trunk), valve cover studs breaking off on their own (anything with an N52), etc...all expensive stuff. It's fairly common knowledge among the techs that I know/associate with, that if you're going to buy a BMW you should either buy new with a top-notch extended warranty, lease it and get rid of it when the warranty is up, or not buy one. Even if you're a tech, or mechanically inclined, the parts themselves that commonly fail are SO expensive that being able to install it yourself doesn't make a difference (especially since you won't be able to program or configure anything yourself).
NOW, in reference to the charging issue...There should be a blue wire going to the alternator. Check with the engine running that you've got 12v going to that wire.
Check the battery, see what static voltage is when sitting and check the CCA available. Also make sure the belt is tight on the alternator, and that the pulley isn't worn out/gouged out. I've seen that a few times, as well. The other thing to check is to make sure the connections on the back of the alternator are good and clean and tight. I believe there are two large red wires and the blue wire, but it's been a while so I'm not certain. Pop that plug off and check them, and make sure the connectors in the plug are snug and not loose.
I chased a similar problem for a few weeks on my 300d, and it ended up being the alternator. The problem with bench testing is they just spin it up super fast and see if it's got voltage - this may mean that it's charging at higher RPM, but not at lower RPM. Test voltage with a multimeter with loads both on and off (high beams, A/C compressor) through the RPM range in 500rpm increments, and report back.
