My smudge battery died, and my so far reliable magicshine is now only lasting an hour before the lamp shows low battery so it’s on it’s way out too.

What’s the best option for batteries and a box to put them in? Quite happy to go with separate 18650 cells, charger and box as I’m guessing it’s probably one dud cell in each battery that’s killing them so replacing them one at a time will be better in the long run.

I’ve been using single 18650 (Panasonic ones). They are so good that two in series will power your magicshine on full power for more than 6 hours. I’ve never gotten round to trying them in series parallel configuration. (I suspect they’ll last twice as long).
I conducted a little test and ran my light over night in the garage. It was still going in the morning.
The only downside, it takes nearly all day to charge them with a nightcore charger. Though, there are probably quicker chargers available.