You can use the 3-5 tunes OR the stock M50 or stock S50 performance tunes as a starting point since you will need to make fuelling adjustments anyway to suit your cam and header mods. You really need a wideband air fuel ratio reading to know what to do with fuel. Some places may be fine, other spots may need more or less fuel, again, it is going to be specific to your setup and the only way of knowing is to know your AFR.
For the timing, you can probably get away with a few more degrees here and there. But, with timing, it is best done on the dyno as you can SEE the changes in power that you might otherwise not really feel on the street when you are doing a bunch of tuning. If timing changes are making a huge difference, you will feel it, but if a degree here and a degree there make 1 or 2 HP improvement, you won't feel that and won't know if your changes are making a difference.