Forget about lithium-ion in your mags for the moment. Your experience with a lithium tool should not be considered useful for handling loose cells of a totally different chemistry than what is in that tool. Keep in mind that their are numerous lithium chemistry cells available, and they all get lumped into the category of "lithium-ion" which is EXTREMELY misleading and reckless by the industry in my opinion. The lithium ion cell in your laptop and cell phone are VERY different from the lithium-ion found in a tool.
For 3 cell flashlights, in C and D size, your best bet is just to get low-self-discharge NIMH cells and call it a day. They will be direct replacements, with good capacity... Get these:
C cells
D cells
Out of curiosity, which NIMH C and D cells are you using currently? And what flashlights are they going in specifically? (I'm going to take a guess that you have some store bought cells with ~2500mAH capacity)....
I have CHEAP NIMH C and D cells from powerizer/tenergy. I top them up once every few months, but they have never let me down and always have a good chunk of juice remaining when I put them into service in power outages and stuff. This leads me to wonder what C and D cells you are using to have had such a bad experience, as most of the better C and D size NIMH cells out there, even the non-LSD cells, are pretty decent at retaining a charge in my experience.