Further, where the red dots in the centre of each pot is, is where we have literally have just sanded back the surface and soldered directly to the base of the pot - have we read that correctly from the diagram? F
On the volume pots, where a connection tab is shown folded so it's on the back of the pot, have you soldered the tab to the pot (on some pots you may need a wire link to do this as the tabs aren't long enough to do this)?
It will certainly make a difference! I'm afraid that it's one of those things that is obvious if you've done it before, but if you haven't, then it needs to be stated explicitly.
Note that the master tone pot doesn't have the unconnected tab wired to anything, as the pot works as a variable resistor (2 connections) rather than as a potential divider (3 connections) like the volume pots do.
Also, it's worth checking to see how many wires there are from each pickup. The wiring diagram shows the details for a two-wire pickup connection, but the factories do change the pickups a bit from time to time, and the kit may have come with 4-wire connections (actually 4 wires and a screen connection). In which case the wires that need connecting will be slightly different to the ones shown in the wiring diagram.