The BCF conversion is going just fine. I have heard big problems are looming with the Bedek/IAI conversion. Assuming the 400 that's being converted had the high gross weight (872,000lbs) then it's not an issue. The increased ZFW is accomplished via the mod. The upper deck is modified aft of the upper deck escape doors and the beams are removed and applicable wiring and controls are re-routed. So there is an increase in the number of full size pallets when compared to the 300.
There are some "soft" spots on the main deck so there is a slight payload issue, however, that's offset by a lower empty weight as there is none of the nose door hardware.
I do know of one 400 operator who had the Bedek conversion done and they are having a very hard time due to some weight issues. They can't market the aicraft and are looking at selling it.