Thanks for posting the values! I did a comparison and the following table summarizes the differences I could find:
[UPDATED]

[UPDATED]
Items in
RED are clear differences. Items in
BLUE are something to further inverstigate, since apparently the Yamaha value is incompatible for the Korg use of this resistor. R2 connects to the node formed by R3 & R10, while its other end goes to the 7-pin connector. Basically R2 allows summing an external voltage to control remotely the Manual setting of the effect, probably by means of an expression pedal. It doesn't affect normal operation and this difference can be disregarded, since KORG devices don't have this modular connector.
Main differences are on the filter capacitor values, both for the upper and lower frequencies (see those 1u changed to 0.1u?--R8 & R16). Also, it seems the two summing resistors for the dry and wet paths (R11 & R18) on the Korg schem were more carefully selected, perhaps to compensate for a slightly over unity volume when the effect is engaged. This leads me to believe that the Korg unit might be a later revision and the Yamaha the original. Another aspect supporting this are some capacitors (c24 and c25) that didn't exist on the Yamaha version, thus were added later to provide extra filtering. The fact of removing the two 51 ohm resistors in series with the clock lines makes sense since the datasheet recommends them only for BBD's with more than 4096 stages (i.e. when a single MN3101 is driving two MN3005's).
Two aspects seem unique to this LFO design. First, the triangular wave is extra filtered by R43+C17 with a cutoff frequency of 1 Hz. This is certainly an aid when the device is used at high modulation speeds for effects such as chorusing and leslie, turning the triangle shape into a milder waveform. I think this is key to the good sound reported. Second, the three diodes in the emitter of Q2 add some nonlinear feedback to the modulation, which might be there to have a more uniform sweep (into the hypertriabgular territory). This last statement is yet unverified, but makes sense with the special sound reported for this circuit.
An interesting question now rises: which of the two versions is better? These gems are rather scarce, so it might be difficult to be able to make a side by side comparison between a Yamaha and a Korg version. Also, proper biasing of the BBD is crucial for good sound. I've read before in the context of the CE-2 that many "average" sounding units sounded superb after retrimming the bias. This means if someone ever has the chance to make such a comparison, proper biasing must be ensured on both devices under test for the results to be valid.
As a closing comment, all the 10k resistors installed on the (+) input of the audio opamps are useless and could be replaced by jumpers, since the opamps (TL062) have JFET inputs thus said resistors don't make any difference in terms of offset voltages.
Regards,
STM.