Have travelled through the Wallasey and Birkenhead tunnels by motorcycle a few times (it's free for motor cyclists) and wondered at the time how it would be to cycle through them. Going down and along the level at the bottom not so bad I'd imagine, but quite a slog climbing out whichever direction you were travelling. Narrow lanes, heavy traffic filling the those lanes, plenty of potential for close passes. You may not notice it in a car, but there's a strong smell of traffic fumes, and the tyre noise and mechanical sounds can be be quite intrusive.
It wouldn't be particularly pleasant for pedal powered transport at touring speeds. Perhaps in the middle of the night it could be an almost surreal, life enhancing experience but even then there's likely to be traffic. A city the size of Liverpool never sleeps.
Otherwise, +1 for the ferry.