Was your daughter born in Ireland or the UK? And has all her education so far been in the UK? If so she will be exempt from studying Irish, which will make life much easier for her. She will be able to use that class time each day to brush up on subjects she is struggling with.
For the subject of history she will need to be prepared for it to be a difficult subject at first as about half of the course will be Irish history and the study of English history will be from a very different viewpoint than that which she is used to. If she finds it interesting though, it's always very enjoyable to get a different perspective. This will also be true for some business subjects as they will focus on Irish trading laws rather than British ones.
Religion may be an issue. There are literally 9 multi-denominational secondary schools in Ireland, 6 in Dublin, 1 each in Wicklow and Kildare (which is essentially the Dublin commuter region) and 1 in Cork. Most other schools are Catholic with a smaller amount that are CoI. There are some ETB schools which claim to be multi-d but they are not, they are Catholic. But you have a constitutional right to opt her out of religion classes if you want. Which to be honest might be a good idea even if you are religious because it would give her an extra class each day where she could work through any subjects that she needs to give extra time to help with the adjustment.
Personally I'd skip the Junior Cert if possible. If the schools you've spoken to are telling you that skipping is an option then I'd go down that route. Let her go straight into Transition Year, which will make the whole change much easier for her and give her a less stressful year to adjust to her quite big transition. If she wants to go to college/university in Ireland, which would make sense as it's so cheap, then she'll need to do a lot more subjects for her leaving cert than she would need to for A levels. Irish, English and Maths are usually required plus an additional European language then another 2 subjects to make up the points for university courses. If she is exempt from Irish she won't need to do that but she will instead need 3 additional subjects. For college courses 5 subjects should be enough to make up the points.
And lastly, on a separate note, do you have accommodation sorted? Housing is incredibly expensive in Ireland again, with even the small cities having extortionate rental costs.