Having a quick skim over that web page, yes it does look like they know what they are doing. However, they are still using SureSelect Whole Exome v4, when v6 has been available for quite some time now, and is so much better than v4. Their mean read depth is decent at 136X - that's about what we do. They quote a 31% pick up rate, where we have about 50%.
They talk about confirming variants using Sanger sequencing, but there is quite a bit of talk nowadays of stopping doing that, because NGS is becoming more reliable than Sanger. The problem with NGS is false positives, and the problem with Sanger is false negatives due to allelic dropout (the strand of DNA with the variant doesn't make it to the sequencer, so all you see is normal DNA). There is some concern that doing Sanger confirmation is rejecting more true positives than it is correcting false positives.
Our lab is both clinical and research. We don't do many research whole exomes any more - mostly doing whole genome instead.
You could mail me at nc74rmec@pliggle.homeip.net if you want. (Yes, that's a throwaway address.) Not sure I can advise you much though.
Separately, can I get in touch with you somehow? I am dealing with clinical genetics as a patient right now, and would love to get some advice.