Bearing in mind that not all Manningtree trains call at Stratford. I believe they are hourly from there (Well the
IC▸ services certainly are)
LST has a half hourly service to Manningtree, One is pick up only at Stratford whilst the other is non stop, with first call being Colchester. The Pick up only trains at Stratford also call at Chelmsford and other places so are slightly slower.
I would discourage the Jubilee line in this instance if I'm honest. I would also discourage the Bank suggestion.
IIRC▸ , Farringdon does have lifts. So luggage wouldn't be a big problem. However getting from the through platforms to the Underground at London Bridge is an absolute pain.
If you take a Southern Fast into Victoria, The quickest way would probably be Victoria Line to Kings Cross and Circle/Met/H&C lines to Liverpool Street. However the Circle is direct, albeit much, much slower! I remember that Victoria is hugely lacking in the lifts department...
I would say that
NRES▸ is working by the shortest possible distance. In which case the routing seems correct. However I can see how someone with more knowledge than a layman might think "Why would one go that way?"