Sorry I'm late to this, I've not been on the forum much lately. Good choice of guitar, obviously! I only play 408s these days and have spent quite a bit of time dialling them in on several guitars.
First thing, don't swap out any of the gold coloured parts e.g. tuners or stoptail posts. They're brass and have all been chosen specifically to give tone/resonance/whatever. Leave well enough alone!
Right, on to the pickups. They're wound with the same wire that's used in the 59/09 pickups and the general specs are quite 59/09-like. I've found that 408s are very sensitive to how they are set - overall pickup height, treble and bass height balance and pole piece balance. They'll need adjusting for your particular guitar (done by ear) but my starting position is:
* Measure pickup height with the last fret pressed down, top of pickup screw to bottom of string
* Top E and bottom E pickups screw edges are level with the plastic bobbin, with the crown/head of the crew rising up out of the bobbin
* Both pickups low E and bottom E are set to 2/32" as an overall height
* Raise the screws for the A/D/G/B strings so that they are also set to 2/32"
From there, I check the overall volume balance of the pickups raising or lowerering both sides of the pickup by 1/4 of a screw turn at a time. Once the volume is about right I'll adjust the bass/treble balance for each again by 1/4 of a turn at a time. I've generally found that I like the bridge 408 flat but the neck pickup higher on the treble side than the bass side (to remove some wooliness caused by the way I play).
I hope that helps?
By the way, here are my two favourites - they're freakin' awesome...
