Boss CS-3 schematic help needed!

[carboncomp]

I would really like to build a Boss CS-3 clone with a bunch of Mods I have found on here, but would also like to remove the buffer or at least the Boss switching to make it true bypass.

Could some one help me with what I need to remove?

[flopoeko]

I´d check R.G. Keens website GEOFEX for the concept of Boss/Ibanez-Flip-Flop and for ways of true-bypassing it.
There you will find an interesting article that I urgently recommend on how to use the already existing circuit (including the footswitch) to control a DPDT-Relais for clickless relais-true-bypass.
No drilling, no clickless-bypass-sets, no 3PDT mechanical switches...It´s worth checking!

[GGBB]

Remove C14 and everything after it up to and including Q4. Reconnect C15 to the level control wiper (where Q4 was). Add your true bypass switching.

[Transmogrifox]

flopoeko is onto something useful here.

GGBB gave the practical run-down of what's involved in the existing bypass scheme, more explicitly listed here are the parts you want to remove:
C14
R25
R26
D7
D8
Q4 (Jumper a short between Source and Drain)
Q5
C10
C16
R19
R24

You could remove that whole flip-flop circuit too if you're doing a mechanical switch bypass:
Q2
Q3
D9
LED
R20
R21
R22
R23
R33
R34
R35
R37
R38
C18
C19
C20
Momentary switch

If you want to do momentary pushbutton true-bypass, then you could keep the flip-flop and set it to drive a latching relay as flopoeko mentioned. 

Whether relay or pushbutton,  your input connection point will be at the IN jack as shown in the schematic, and output will come from the OUT jack.

Follow any schematic or layout for a DPDT true bypass.  If using a relay you don't need to add the millenium style LED indication circuit to the TBP switch because the flip flop has you covered for LED on/off status.