Before we can help you trouble-shoot any problems, we'll need a diagram of how you have this wired at present. It looks like a beautiful guitar!
The double-neck guitars that I have seen use a 2-pole switch (a DPDT) to switch the outputs of the two necks- each neck has a "hot" and a "ground" going to the output jack, and the selector switch simply sends one pair or the other to the jack. This way, only one neck is "on" at a time.
I can also visualize that, with a bass as one-half of the thing, one might want a separate output to go to a bass amp. A 4-pole switch could then be used to switch outputs.
The guitar has similar setup with 2 humbuckers with 2 Volumes and 1 tone.
That's not what your diagram shows. On the soapbar HB, you seem to be showing a pot used to split the coils (the so-called "Spin-A-Split"), with a single Volume and Tone after it. This seems to be a part of your problem, as the "Spin-A-Split" is then wired to the V and T controls. The wire coming out of the "Spin-A-Split" needs to bypass the V and T controls, and to be wired either directly to ground, or directly to the "hot" output (i.e., to the guitar/bass selector switch). Which way you go depends upon which coil you want to be the one that is split. (I can't tell you which one is which without knowing the pickup mfr and wiring colors.)
Also, look at how you have the V and T controls wired for the HB. You show the input to the V pot going to the clockwise lug of the pot (if looking at it from the back of the pot, which is the usual way to depict guitar diagrams). The output then goes off of the middle lug (the "wiper").
Compare that with how the V and T controls are shown for both the soapbar and for the bass side of things. There, the input to the pots goes to the wiper instead. A volume control wired in this manner will never go to "0".
So, I would suggest rewiring all of the controls just like you have the HB wired.
Finally, on the bass side of things, you do show individual V controls for each pickup, with a master tone. Since you don't seem to have a switch to switch pickups on/off, I assume you're using the V controls to turn the pickups on/off. Apart from rewiring the controls, as discussed above, you may want to consider using a dual-gang pot for the master tone; this allows each pickup to have a separate "gang", and avoids interaction between the 2 volume controls. JohnH has a thread in the Schematics section called "Strat with 2 Volumes" that describes the problem of the control interaction, and the solution using a dual-gang pot for the "master" tone.
Hi Thanks for your info, I finally got it to work. Now my next question is am i able to run active bass pickups and passive guitar pickups. The guy at the local guitar shop who wasn't interested in helping me with the wiring said it wasn't possible.
Surely the toggle switch would just seperate the two?