Yamaha CD S1000 or S2100 as transport

@output555 In full transparency I am a dealer (and audiophile first) but do not represent or sell Yamaha.  I’ve owned both units but didn’t A/B them to an external DAC, so take this with a grain of salt. 

I’m actually not convinced that the drive trays and transports are all the same in both units, even though they look the same. I know the 2100 has the same transport as the flagship 3000, so there may be some bracing improvements etc that help it to perform better. Also:

1. The 2100 has slightly better cabinet bracing for improved stability and vibration reduction overall. 
2. The 2100 has improved power supplies, and two of them, one dedicated to digital signals and a more robust supply for everything else. This may result in a lower chance of ripples in the current which result in more clarity in the transport’s performance. 
3. The 2100 is considerably newer. Dealing with the 1000 means having a transport that has been manufactured and/or used for 14 years. Yes it looks like the unit can still be purchased new, so that would be your better route if you do go for the 1000.
4. The 2100 has a DPLL function. While the manual states this is in the DAC, it should be tied to the internal clock and not through the DAC stage (I could be wrong but I think the manual just wants to make it easier for people to understand even if not entirely true). Since the only options for digital output are spdif (Toslink and coax), it will use the internal clock of the 2100 and likely keep the DPLL setting, which may add to the snappiness of the sonics. 
5. If you didn’t want to use the digital out, the internal DAC is considerably better, and the 2100 can also be used as a USB DAC on its own. Very useful should you decide to simplify the chain down the road.

If it were up to me, I’d swing for the 2100.

Thanks very much for the honest and thorough reply.

You have confirmed what I suspected about the S1000's transport: It's the same, but different. Given the significant price difference between the S1000 and the S2100 some compromises would have to be made besides the downgraded DAC. I've looked at photos of the innards of all three players, and there are differences in parts and architecture. The S3000 and S2100 are the more premium, the S1000 somewhat less so. That said, compared to other players in the $1500 price range, the S1000 is built like a tank.

I'm taking your advice and going for the S2100. 

Thanks again!

Since you have an external DAC that presumably you enjoy have you considered any dedicated CD transports instead of getting a CD player? In the price range of the Y 2100 there's Simaudio 260DT, Jay's Audio CDT2, and Denafrips Avatar to name a few. Thought here is that you'd be putting the money towards a unit that is maximized .for its sole purpose versus one with effectively a couple of purposes. I have the Sim in my 2nd system . Anyway just a thought , good luck with whatever decision you make.