In terms of the stations...
The new platform at Limerick Junction will be opposite the main platform (used by Cork/Dublin trains). I quote from the site notice
"The development will consist of the construction of a new platform, including passenger shelters and furniture, platform lighting, fencing and drainage and all associated works - to the north east of the existing platform(s). The new platform will be accessed via a new covered passenger footbridge, with 2 no. stairs and 2 no. lifts. Ancillary platform equipment including customer information systems and signage, will be provided on both the new and existing platforms. Limerick Junction Railway Station is a protected structure."
Not sure but would imagine the track may be reconfigured - someone else may be able to assist with this info.
A previous thread on the topic
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.