Provided the engine is vaguely sensibly sized there will be very little or no difference below 20mph as everything is limited by weight on the axles (unless the engine is very puny.) but 3 phase traction equipment should improve on this.
Which 66 timings -e.g. how heavy/ long is the train? Easier to get near existing timings with shorter trains...
As speeds on the branch don't get that high you might not need that large an engine especially with more efficient traction electronics. the 88s/93s use a CAT c27s (950hp) but the sensible (and Stage V certified) choice from CAT for the 99 is probably the 3516E at 2100hp
Speeds not high but the branch is very stop/start so smaller engine would affect acceleration. Plus the bank climbing up from Ipswich to Westerfield and out of the terminals.
You could solve that one by electrifying from Ipswich to probably just beyond Westerfield (so the electric to diesel changeover happens on the level) - maybe just do the 'uphill' track if money is really tight.
But surely the Felixstowe branch has to be one of the busiest and therefore most profitable routes for Network Rail. Ergo it should be electrified soon - towards the top of NR's plans. The passenger trains are already able to run under 25kV, and FL, GBRf and DBC all have AC locos which could work through to the port. In this instance it is crazy to even think about battery Bimode locos and Felixstowe in the same sentence. There needs to be an East-West spine as follows
Felixstowe-Ipswich / Bacon Factory
Haughley Junction-Ely Dock Jn
Ely-Peterborough.
Peterborough-Syston Jns
Wigston-Nuneaton
Nuneaton-Grand Jn / Proof House Jn
In conjunction with the MML electrification this would provide through electric traction for anything out of Felixstowe towards London, but also to the ECML north, the MML north and south, the WCML at Nuneaton, inland container ports at Hams Hall, Lawley St, Cannock etc etc
It would also allow the Birmingham - Leicester - Ely - Stansted Airport passenger service to be turned over to EMUs and probably BEMUs for the Nottingham - Norwich service too - assuming Nottingham-Grantham and Ely-Norwich is achievable with batteries. It would allow some Bimode class 755s to be replaced by straight EMUs and released to other lines where Bimode is useful.
The "stones throw" Manton Jn - Corby should also be wired to allow both freight and passenger services.