Limerick J will be like Kildare and have 3 running lines between both platforms (loop up), (up fast) and (down fast). Access to the current main platform will be maintained after the new one is added and like Mallow when possible up/down will be via the loop to ease connections.
The proposed relocated Waterford (Plunkett) station would be a few hundred metres along the South Wexford (Wellingtonbridge/Rosslare) line east of the current station.
As there is already some "padding" in the timetable (charter minutes as they were termed some years ago in the UK) particularly southbound to Waterford from Thomastown there is no reason journey times on the Dublin line should increase (they shouldn't increase on the South Tipp line either). The approach to Waterford however is rather slow and perhaps this can be looked at as part of the overall project.
On the assumption there will be a new CTC signalling system, there would be no justification for longer journey times and 50 mph + should be allowed towards Waterford West with complete relay but knowing Irish Rail I wouldn't put an extra few minutes past them.