I've gone back to using Tyler's Hungry, Thirsty, Sleepy, Tired and despite it showing two entries of conflict in TES4Edit, it seems to be behaving with the rest of my mods now.
I must've played 10 to 20 hours with this semi-final load order
Spoiler Oblivion.esm
Unofficial Oblivion Patch.esp
DLCShiveringIsles.esp
Enhanced Economy.esp
MD_Saddle_Bags_Lite_v2.esp
MD_Saddle_Bags_Accessories.esp
HorseCommands.esp
MD_FasterHorseTurning.esp
Knights.esp
The Lost Spires.esp
Harvest [Flora].esp
Harvest [Flora] - Shivering Isles.esp
Bag of Holding.esp
DropLitTorchOBSE.esp
P1DkeyChain.esp
SetsunaDummyTraining.esp
Toggleable Quantity Prompt.esp
Tyler's Hungry, Thirsty, Sleepy, Tired.esp
Denock Arrows.esp
Let There Be Darkness - Cyrodiil + SI.esp
I think I've tested this configuration enough and will install Map Marker Overhaul to see how it behaves with it.
I guess my main sources of CTDs previously were Alchemy Advanced, and/or Thieves Arsenal, and/or simply using the Shift- transfer all function in TQP far too rapidly.