Not much of a response here

. I get that, it's not really groundbreaking either to just miniaturise an existing pedal.
However, I went ahead and converted the SC to MN3207. This meant redesigning the power supply for the digital parts, which isn't as simple as on a CE-2 where the Egg for the BBD is provided by the clock. I'll let the schematics speak for themselves when it comes to the other changes.
The first schematic is the most basic one with a simple zener regulator and intended for 9V use, with 9V max provided to the BBD. Should be safe for the BBD and in the optimum working range of the MN3207 (IF I understand the datasheet correctly; minimum THD at around 8V operation).

The second schematic is with a 7809 or 7805. Both should work, but when supplied 9V the 7809 will drop 2V and the BBD will run at a lower voltage.

The third schematic incorporates other changes as well. The digital components aswel as the bias for them runs of a low noise LDO regulator. The LT1761 has a max voltage drop of just 150mV when loaded as lightly as in this application. I ditched D2, which only provides a unnecessary voltage drop after Q1. Not needed as I used a NPN here and not an PNP. More true to the original would to use a PNP for Q1 and use D2. I just can't seem to find the reason why it was done that way.
The biggest change however is in the parts surrounding IC1. The MN3207 has a fair bit less dynamic range when compared to the MN3007. The SC by default boosts the high frequencies in IC1a by as much as 18 dB and compensates for this in IC1b. The Boss CE-3 is much tamer at this point and boosts the highs around 10 to 12 dB. To me that seems more reasonable and get some of the headroom back. All was simulated in LTSpice and by the end of the signal chain, the frequency characteristics between my tamed and a stock SC are the same. Apart from an obvious noise penalty, is there any reason to tame the signal to the BBD?
