I'm confused.
The named services I mentioned above were the boat trains that always started and finished at Harwich Parkeston Quay and, when they were no longer routed via the NLL and WCML, would have passed through Ipswich. However, Ipswich already had it's own rail links with the Midlands and North-West as part of the BR (and later Provincial Services) XC network in addition to, and independent of, the boat trains.
But to answer the specific question in the original post, no there were never trains from Manchester to Ipswich or Felixstowe to connect with the boats to Europe, as the boats did not sail from either of these ports. Yes there were trains from Manchester to connect with the sailings, but these went to Harwich PQ (even though many would have stopped at Ipswich). Additionally, yes there were also regular trains to Ipswich from Manchester that had nothing to do with the boat trains.
I expect you already know this, but the Ports of Felixstowe and Harwich share the same stretch of water, facing each other from opposite sides of the Stour Estuary. Harwich always majored on passenger traffic because of it's quicker links to London via the Great Eastern Railway, where passengers from Felixstowe had to get to Ipswich first for connections to London.
O L Leigh