Cheers!
I've basically fixed the intonation problem. I think it arose from the TOM tailpiece being too low relative to the bridge, and the strings touching the back of the bridge. My eyesight is poor so I didn't notice that before I first played it. Took my glasses off and put the guitar up near my face and I could see it and adjust appropriately. I also lifted the bridge enough to get rid of almost all the buzz but there is some somewhere, which might require a truss rod adjustment. I'll show someone tomorrow and see if they have any ideas, and at worst it might require a trip to a tech (it needs some fret adjustment anyway, and I could ask him to install that bridge ground wire when it arrives).
The issue I am having is pickup height. I have been getting a woofy and wooly sound out of both pickups, even though it is very clear that the output is increased relative to the 490R/498T set. I have raised the pole pieces half a turn on each pickup, which combined with lowering the pickups seems to have improved things. The neck pickup looks very low now though. I'll post some photos of it before and after so that people can compare them.
If anyone can give advice on the distance from pole piece to string that they find works well with the Cold Sweat neck and A-bomb bridge that would help.
I have the long legs and chrome covers. So far the bridge pickup is not poking out. It may actually be lower than stock. I'll have a look at the photos and see if I can tell.
I'll update this post in a little while with photos
EDIT: Actually I might post that over in the tech part of the forum to get a broader range of advice (click
here).
Here are some photos of the old and new components:
490R/498T set (note the connectors and the discoloration - heritage cherry? - under the neck pickup):

2011 PCB Gibson wiring:


Vintage style harness from SCS Custom Shop:

BKPs (Cold Sweat & Nailbomb, R-> L):

Pickups installed:

Harness installed (note the temporary wire to connect the hard copper wire from the PCB to the pot - that wire was originally in the green socket on the PCB):

Basically I bent the wire into an eye and then wound the brass (silicone covered) wire around it and then added a large amount of solder to that (birdshiteee style), soldering the other end to the pot. It looks messy but does the job until I can get a new ground wire from the bridge to the volume pot fitted.
I reused the Gibson pickup screws and springs for a few reasons. First, I managed to lose one of the new springs. Second, the BKP screws were slot heads rather than the original philips head type (I'm trying to keep this looking as original as possible). Third, the new ones were just so springy that I found it easier to get the old ones to compress (as they had already been compressed for over a year). The bridge ground wire and the springs pinging off everywhere were the two difficulties I had. The rest of it was straight-forward enough. I just need to get the pickup heights sorted now.