First of all, going from two 250k tone controls affecting all pickups to a single tone control of 250k each on bridge and neck (and consequently no tone pot on the middle pickup) will make things a lot brighter, thus giving the sonic appearance of having less low end.
It seems what you have now is the following:
A guitar made of rather bright sounding woods.
Pickups:
Anni 36 bridge
Area 67
Injector neck
VV Heavy Blues 2
Pots:
2x 250k
1x 500k
Tone caps:
0.022uf
0.047uf
Issues: bridge pickup too bright, both Injector neck and VV HB 2 not stratty enough, positions 2, 3 and 4 too bright.
Well, it's no wonder, the Area 67 with a 500k volume pot and no tone control wired to it will be piercingly shrill. The Area 67 to my ears works best with a 250k volume pot, which should also work well with the 36 Anniversary bridge (at least it does work well with the Virtual Hot PAF in my strat). However, both the VV HB 2 and the Injector need a 500k volume pot to sound their best - with a 250k volume pot they would even sound less stratty.
If you want to stay with the 36 Anniversary bridge, I would use a 250k for the volume pot, a 500k pot with the 0.022 cap for the bridge pickup and a 250k pot with the 0.047 cap for the neck pickup (or alternatively one 500k tone control with a 0.022 cap). I would put the Area 67 in the neck position, sell the Injector neck and the VV HB 2 and get an Area 58 or Virtual Vintage 54 Pro for the middle. This set up would be very close to what I use in two strats and would get you the stratty tones in positions 2 - 5 and a not too bright bridge humbucker.
Alternatively, if you are willing to go to a stronger bridge pickup, I recommend to use the 500k as volume pot, put the VV HB2 in the neck and the Injector neck in the middle. Sell the 36 Anni and the Area 67 and get an AT-1, AirZone or any other hotter humbucker that you like. You can use the 250k pots as tone pots. But since you say that the VV HB2 and the Injector neck are not stratty enough you may consider the first set up described.
Here is a diagram which could be used as a starting point:
http://www.dimarzio.com/sites/default/files/diagrams/1h2virtualv5w1v1nbtone.pdfI have not found a diagram for two tone controls but it is easy to convert this one to that. See where the connection from the tone pot goes to the switch. See also the connection from this lug on the switch going to another lug on the same side of the switch. Remove that connection and go from the other lug to another tone pot and wire that up just like the pot in the diagram. Any competent tech should be able to do that.
If you want only one tone control, you could use the following diagram:
http://www.dimarzio.com/sites/default/files/diagrams/1h2virtualv5w1v1t.pdfGood luck,
Stephan