Also make sure your patch cables are decent. I had noise issues, invested in a Cioks DC5 (which is brilliant by the way), and when I rebuilt my board testing each element in isolation I found my noise issue was due to the poor shielding in EBS patch cables picking up noise from my dimmer switch.
There are two main issues you get with daisy chains. If a pedal has positive ground / reverse polarity it can either introduce really obvious loud buzzing / squealing sounds or cut out sound altogether. Secondly, and more commonly, some digital pedals might leak noise into the daisy chain which is then picked up by other pedals in the chain. To test this out, put all your known good analog pedals in a chain and then try introducing one digital pedal at a time. Listen for increased hiss, or digital clock noise which sounds like chirping - you might not even have to put the pedal in the audio path to get this, just have it on the daisy chain.
A true bypass looper is useful for testing to see if any long leads or patch cables are the culprit also, you can pick one up for about £15 and you might find it useful later on if you want to use a pedal that doesn't have a great sounding bypass, or as a patch bay to escape your entire fx chain in case something dies on you!