It's certainly an interesting topic.
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I don't use the digital I/O at all, but it doesn't surprise me that when you use the Kemper as a master, your other convertors don't quite sound as good as they may when you use higher-end and dedicated clock masters. This is, after all, is why the Big Bens of the world exist; there's been a market for these things for eons simply because proprietary (in-built) clocks of our various outboard devices aren't specified to perform the task at the cutting-edge of technological possibility. They're generally there for their utility - to be used in a pinch, but certainly not as permanent solutions in pro setups.
This wouldn't be an issue at all if it were possible to set the Kemper's clock to an external source. Sure, Big Ben's/etc exist but if the Kemper's clock is causing noticeable issues to my system, then it'd be nice to have the option to sync it somewhere else. FWIW, I'm not using any kind of dedicated outboard clock, and this is the only time I've noticed a perceivable drop in quality when using digital devices (compared against "cheapish" units such as MOTU 896HD/Mackie Onyx/Focusrite Forte). It's not so much of an issue when only using the Kemper by itself - more of an issue when recording multiple instruments at once, or working at different sample rates. With the most recent generations of converters, the benefits of external clocking has reduced fairly considerably (the Big Ben for instance has been discontinued). If the Kemper isn't equipped with a clock that compares favourably, even to standard interface clocks, then it would make a lot of sense to be able to run the Kemper as a slave to whatever the best sounding option is.
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As for the DI thing, which was your main focus, I suspect that the plain-jane feedthru (guitar-level) is for all intents and purposes uncoloured
I'm curious to where the "uncoloured" assumption comes from? Connecting a guitar to any kind of "load" is going to affect how the pickups react - if the impedance is too low, the high end will disappear (good luck getting that information back). Likewise, all DI's have a frequency response, noise/THD behaviours, dynamic range etc. These values are not provided by Kemper so "uncoloured" is baseless without some kind of reference point. It certainly fares better to me than my Little Labs Redeye did (lower impedance than the Kemper, caused loading to the pickups and a lack of high frequency information). I've also used DI's that cause the high end to become distorted and lack clarity resulting in noise from around 3k upwards - again the Kemper
doesn't seem to suffer from this. Furthermore, the specs given from Kemper (although by no means bad) compare less favourably to other gear; if you deem the Kemper to be uncoloured, then by definition choosing equipment with superior specifications will provide even less colouring.
What I have experienced, is compared to DI's with a higher impedance than the Kemper (2.2MOhm upwards, such as http://rupertneve.com/products/rndi/#tech-specs , http://www.creationaudiolabs.com/#!mw1studiotool/cp99 , http://www.uaudio.com/interfaces/apollo.html , etc), the Kemper has less information in the high end (a warmer tone). This may not be an issue with lower output pickups or if the intended tone is on the warmer side. When capturing my DI's, I'm looking to capture as much of the sound as possible rather than losing anything.
Now as far as splitting your signal goes, a good DI box is critical here as its impossible not to affect the impedance - hopefully you have the opportunity to try a few different ones (and even compare to the Kemper's) so you can experience what I'm talking about. The MW1, for example offers a variable impedance on input and output which seems like it would be great for tuning the impedance to the desired guitar sound. The Rupert Neve DI has the ability to also be used a speaker load which obviously has its benefits for making direct profiles. I'm currently going directly into the Apollo DI and then in and out of the Kemper which has the benefits of only one A/D stage, and also keeps my analogue inputs free for other things.
Now, I'm sure we can agree that its best to not blindly assume that the Kemper (or any piece of gear) is the absolute benchmark in DI's, A/D conversion, clocking, etc. I'm not saying it categorically isn't, but based on the specs they've provided, it certainly doesn't stack up as well as other equipment. That's not to say that if all I had to work with was the Kemper, I wouldn't just get on with it, but given the other equipment available to me its worth exploring various options and working with the best sounding AND most convenient workflow. I started this thread as I was curious if there was people out there (say with one of the DI's I mentioned, or equivalent) who had experienced something similar to me, and I'm still interested in how others may be incorporating such equipment in their set up.