I would wire the chasis together first before bringing it to the guitar. This wwould be all the interconnecting pots and switches in one central area. Keep the pickups and whatever goes in the holes in the horns separate.
Switches...it's totally up to what you want and what pickups you get. Coil tapping only works on humbucker-esque pickups (ie. 2 independant coils and generally 5 wire is prefered). If you put regular humbuckers in it , for example, you could have one switch be a three way (each pickup or both) and a two way acting as a coil tap. I referenced dogearred P90s last time...I dunno if these come tap'able.
What I'd do (for my needs) is wire together a vol, tone, and output, and have a long lead wire hanging off it. Feed one string thru the Vol pot hole, out the F-hole, and around the vol pot. Likewise another string with the tone for the tone pot. Then pull them thru lock'em down and no more messing with those. Take the long wire run it inside to the top (near strap button) switch area and cut off excess wire leaving maybe 1-1.5" protruding from the hole to work with. Attach this to output of a three way. Install pickups...run hots to 3way removing (or securing with twist ties) excess wire where there is only the same amount of 1-1.5" wire protruding. From there attach separate wires to the coils. There are 2 per pickup...this allows the pickup wire to remain intact rather than "V"-ing it all the way from the pickup itself. Run this wire to the other switch area. Use same amount of wire protruding, and wire for coil tapping.
Thats what I'd do--you can do whatever your heart desires. Also I've never used the Jaguar/Jazzmaster switches before so I don't know if it will work like a regular push pull pot. If you need more knobs you could also get concentric pots and add another tone or volume.
OR you could wire it Gretsch stylee and make the switches tone circuits and make the bottom hole a 3 way toggle.
There are many possibilities...you just need to figure out what sounds you need. I just happen to have a bit of geetar-A.D.D. so I need every possible combination. Well for a while...until I get bored of the guitar and start another project.