I don't know if it's something Cool Edit Pro, etc., support, but I found a useful program called Wave Repair which is specifically designed for aiding the transfer of vinyl to CD. It has pop and click detection, but also allows you to manually redraw the waveform to eliminate such artefacts - rather than doing it automatically. I have used it with some success in the past for transferring some official LPs - but the pop and click removal process can be so labour-intensive that sometimes I've just given up and bought a cheap copy of the CD re-release! Find it at
http://www.delback.co.uk/wavrep/ (demo version that works for 30 days or something, before you have to register it, unless you just want to use it as a hard disk audio recorder).
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