Some opamp clipping can be expected in the Bare Bones Klon (and even in the original although less obvious), have a look at this from the original Bare Bones thread on FSB
http://freestompboxes.org/viewtopic.php?f=13&t=7526That's why a TLC2262 was used, because some people feel rail to rail opamp clip in a more pleasant way than other common opamps like the TL072 or JRC4558. What I would suggest is swapping IC2 to something different like a TL072 and see how it affects the decay you're getting. If it sounds different to what you got with the TLC2262 then you know that it is just opamp clipping that is responsible.