How'd you make the schematic?  It looks great.

The output caps are already 10uF which should be plenty large.

Up the input cap to 10uF and it should be fine for bass.  As far as the tonestack goes, I'm not 100% sure, but I think you'd be fine.

I don't think you can use that...on that same note, I don't think I've ever seen a transformer with only two secondary wires.

2amp slowblow.

I'm guessing that must be it.  Did you check out the pictures I did in the documentation?

I dunno, I never use the neck pickup on the guitar I have now.  I really like bridge pickup sound.

Les Paul Standard?  I've been looking at getting a Epi LP JR.  I need to find a place around here that carries them so I can play one.

Sounds good to me!  I especially like the MPF102 clips, mostly the humbucker.  What type of guitar is that?

I know I've seen rack enclosures for $25 or something at partsexpress before, but I can't find them now.  I did find a rack shelf you could use though:

http://www.partsexpress.com/pe/showdetl.cfm?&DID=7&Partnumber=262-801

$22 isn't bad.

You could use a rack mount enclosure for $20 or so then bolt that into a wooden enclosure.

I would double check all the solder connections are solid.

Well, it sounds like you're good to go.  Keep us updated!

Are the diodes put in the right direction?

You shouldn't be going through transformers like that, and a 12.6 - 0 12.6 should give you about +/-17.5v