Robert S. said:
Kent has got it right, but maybe I can clear it up a little.
A P-90 is a single coil. When using a single coil pickup connecting either the black or white (start or finish of the wind) lead will not change the tone of the pickup in any real way. The reason that one pickup is using the black and one is using the white is in fact to create a rw/rp situation to cancel hum.
The ground to the baseplate should always go to ground irregardlaess of which lead it is paired to. If you wire the ground wire to hot, you'll turn the baseplate into an antenna and you'll pick up all sorts of noise.
Assuming that you have the pickups installed in the correct positions changing the bridge and neck pickups physical position in the guitar will probably make the problem worse. Bridge pickups are usually wound a little hotter and have a slightly lower resonant peak. This makes the bridge model pickup a little darker than a neck pickup. Putting a neck pickup in the bridge position would be to put the brighter pickup in the bridge slot.
There really is no hot lead for a coil. There is a start and finish lead though and these are used to keep track of the wind direction of each coil. With SD single coils the black is the start lead and the white is the finish lead. Having the bridge black lead connected to hot on the guitar and the white connected to hot on the neck pickup is proper to create the rw/rp condition with SD single coils.
Both pickups are correct in their lead wiring.
The only ways to correct the "little too thin" condition you are describing would be to move the bridge pickups location away from the bridge, get a hotter/darker voiced pickup, or if by too thin you mean too bright you could try a lower value potentiometer in the bridge position to darken it up.
You say the guitar is home-made but that can mean several things. If you can get near a factory made guitar with P-90s in it, measure the distance from the pole pieces to the bridge on that guitar and your guitar and compare specs. Pickup location in a guitar is critical to tone.
If you also have humbucker loaded guitars and your amp is dialed in to those instruments, you may need to re-dial your amp to get the P-90s to sound right. Raising and lowering the bridge pickup in relation to the strings can also have an impact on tone. You may want to raise the bridge pickup closer to the strings.