Good luck with your project onehander! You may want to start a new thread to help find the answer to the lost phono/aux signal. There could be many causes, and I am not an EE, just a retired musician with a hobby interest in old amps. The KR-5600 uses op-amps in the preamp section, of which I know nothing, so ask those who do. It is also recommended you thoroughly clean the controls and switches and inputs with deoxit, it can solve mysteries sometimes. I was told not to deox the little button switches (top row) in the glass.
As for the BOM, I am working on it, but with two caveats - first, I only swapped electrolytics in the PS and the Audio boards, not the muting or FM boards, and not the preamp. Secondly, Trio/Kenwood made several changes to their receivers throughout this period, some documented, some not, and even in my two receivers there are different PCB's. So this makes it hard to create one BOM that will fit every KR-5600. I will try to list what I did, and for what model boards, and that is the best I can do. The list will need more contributors. There is also considerable discussion about sizing and fitting different main filter caps, so look around AK for that.
Finally about the service manual. It has been noted hifiengine et all lack this manual. I took a chance and paid for a "manual" from a foreign supplier, and I got a good listing of bias adjustments for many models, and a better copy of the schematic, with several models of the small PCB's. I was disappointed for as much as I had paid, but the good schematic did prove useful. i would be happy to share the s/m with you, and the bias is 40mv.
Good luck with the project, and welcome to AK!