If a flyover on fen is going to be a problem, then rather than one for southbound heavy freight, could we consider one for northbound passenger traffic towards Norwich and Lynn.
You would need to relocate the junction towards Ely and quadruple a short section (on the East side approaching the existing junction). It wouldn't need to carry freight, so would be much shorter and lighter.
The existing North junction would need to remain to cope with freights to/from Lynn and Norwich, but ATM that's just the handful of trains daily using the West Curve, so you have eliminated 90% of the conflicts.
You would need to relocate the junction towards Ely and quadruple a short section (on the East side approaching the existing junction). It wouldn't need to carry freight, so would be much shorter and lighter.
The existing North junction would need to remain to cope with freights to/from Lynn and Norwich, but ATM that's just the handful of trains daily using the West Curve, so you have eliminated 90% of the conflicts.