Placing them in an effects loop is not a good idea - most of these pedals will not work well in the effects loop of your amp, and you'll get distorted sounds instead.
Adjusting the Level knobs on your pedals DOES make a difference. If your clean sound is quieter, the answer is
obvious -
adjust them so everything's at unity gain.
Now, if you're comparing the sound and volume of your bass plugged directly into your amp, to the sound of the bass going through the effects chain into your amp (all effects turned off), then it's a different story. In that scenario, I spot a few culprits:
Quote:
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Bass -> Boomerang - Cry Baby - Boss Phaser - little big muff - aphex punch factory - boss bass synth - mini Q-tron - EBS octave -> Amp
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Those pedals in bold aren't known to have great bypass systems. The Crybaby pedals in particular are known to cause some tone and volume suck. I don't know anything about the Boomerang's bypass quality, so I can't comment on it.
The easy fix for that is a true-bypass loop pedal; it can remove all effects in the loop of that pedal completely from the signal path, as if they were never there.
I should also mention that you should expect a minor difference when running 50 feet of cable + effects, as opposed to running some short 10 foot cable from your bass directly to your amp...