I was never able to resolve it. I even bought another Blueberry clamshell unit, which was sold cheap as "untested, parts-only", which works fine, but has the same behaviour where it will only charge while sleeping. So, I have accepted this is how things are going to be.Hello,
have you solved that diode issue with the DC-in board yet? I'm also working on a non firewire blueberry iBook G3 and got the same symptoms - the D1 was blown. I've replaced the diode and the supercap but that didn't make any difference even for me. I've even rebuilt the battery and to my surprise, it also stopped charging and it's stuck at 0% now 😂. I don't have a TiBook tho...
In terms of the battery. I have repeated the trick where I had the Titanium charge it from absolute zero successfully. For some reason, the Titanium charger has been able to successfully revive my completely dead iBook clamshell batteries.

Here I am powering a 65 watt Titanium logic board, with DC-in and the charge connector, then left it like this to charge for a few hours (not running) and the original, non-rebuilt, iBook clamshell battery came back to life. The bulk of the original battery housing does not fit into the battery bay like it did with my naked rebuild in the earlier photo (a few posts back).
Maybe the charge board from another 65 watt capable PowerBook G4 (or maybe even iBook G4?) could also work? I haven't tested any other config as this Titanium logic board was my most convenient to setup.