Hi,
I also have an Apollo 1240, the 40Mhz version with 64MB. As for stability I get mixed results, but that might be from the fact that I'm also using a FastATA MK2.
Boing2 and Remapollo can be problematic. I've stopped using remapollo in the last days because with boing 2, if I had to reboot my machine from OS3.9 I had either to switch it off or make several quick resets to clean the rom stored in ram, otherwise the machine would show a yellow screen on boot, and I would have no fast mem when loading the OS. The only way to avoid this and keep boing 2 with remapollo would be not to load the OS_Module2 (Exec 45.20).
There is no way you can run Dopus 4.16 with WB31, kickstart 3.1 for amiga 1200 (40.68) and a 68040 CPU! You can check it in Win UAE also, It will always crash! On, the other end in OS3.9 it works, as it does also on WB3.1/WB3.0/K3.0 so it must be a problem arising from kick3.1/wb3.1, not the apollo 1240 itself.
However, since I also own an Amiga 500 with kickstart 3.1 (40.63). I've extracted the rom Image and tryed it in winUAE. With this rom DOPUS works with a 68040 CPU in WB 3.1!
Whdload used to be more problematic. But if properly configured it will work most of the times (some times you also need to use NOCACHE).
Regards