custom true bypass effect loop station tips

[DrFundies]

i'm building a line selector/looper/whatever you want to call it.  I have 12 pedals, some w/ true bypass switching, some without.  My question is... Would it be more efficient for purpose of SOUND QUALITY to build a seperate loop for each pedal ( 12 seperate loops and 12 switches) OR is it better to make 7 loops, one for filter effects, one for distortion, one echo etc... And mod each effect pedal with a true bypass switching system?  Please help!!! 

[formerMember1]

why not just mod some of the pedals for true bypass?
What pedals are they?

[DrFundies]

the ones that are not true bypass are boss, ibanez, and a moog