So I have it all working - thanks to everyone who helped.

 Page 1.png 
(19kb) downloaded 32 time(s).
 Page 2.png 
(24kb) downloaded 28 time(s).
 Page 3.png 
(29kb) downloaded 32 time(s).
 Page Field Names.png 
(25kb) downloaded 31 time(s).GTDesigner - see above for screenshots
Transition in – everything hidden
Page 1 – ScoreBoard Only
Page 2 – ScoreBoard plus Normal Timer
Page 3 – ScoreBoard plus Additional Time Timer
5 Shortcuts (streamdeck)
1 – Scoreboard Only			ScriptStart	ScoreBoardVisible
2 – 1st Half				ScriptStart	ScoreBoard1stHalf
3 – 2nd Half				ScriptStart	ScoreBoard2ndHalf
4 – 1st Half Extra Time			ScriptStart	ScoreBoard1stExtra
5 – 2nd Half Extra Time			ScriptStart	ScoreBoard2ndExtra
Scripts:
ScoreBoardVisable
Function=OverlayInput1IN&Input=ScoreBoard
Function=SelectIndex&Value=1&input=ScoreBoard
ScoreBoard1stHalf 
Function=ChangeCountdown&Input=ScoreBoard&SelectedName=Clock.Text&Value=00%3A00%3A00                (this sets the start of the timer, so 00:00 for 1st Half, 45:00 for 2nd half etc)
Function=SetCountdown&Input=ScoreBoard&SelectedName=Clock.Text&Value=00%3A45%3A00                   (this sets the end of the timer, so 45:00 for 1st Half, 90:00 for 2nd half etc)
Function=ChangeCountdown&Input=ScoreBoard&SelectedName=Additional.Text&Value=00%3A00%3A00           (this sets the additional timer start back to 0)
Function=SetCountdown&Input=ScoreBoard&SelectedName=Additional.Text&Value=00%3A55%3A00              (this sets the additional timer end back to 55 - just so it does not set off oncompletion)
Function=SetText&Input=ScoreBoard&SelectedName=Half.Text&Value=45:00+                               (this just sets the additional time visible (left side))
Function=StartCountdown&Input=ScoreBoard&SelectedName=Clock.Text                                    (this starts the timer)
Function=OverlayInput1IN&Input=ScoreBoard                                                           (this sets the scoreboard input to overlay 1)
Function=SelectIndex&Value=2&input=ScoreBoard                                                       (this sets the scoreboard to Page 2 - which is the normal match clock)
Repeated for other halves, with adjustment to time in 1st 2 rows (starting time, ending time eg 45:00 to 90:00
NB 90 mins needs to be 1 hour 30 mins
Scoreboard – Triggers
OnCountdownCompleted	selectindex	scoreboard	value = 3
OnCountdownCompleted	ChangeCountdown	scoreboard	value = 00:00:00 (for additional text)
OnCountdownCompleted	StartCountdown	scoreboard	value = 1 (for additional text)
This selects Page 3 (Additional Time), then sets Additional Timer  to 00:00, and then starts that timer
This may not be the most elaborate way of doing this (but significantly better than other options i had originally) - and most 'competent' coders will probably be pulling their hair out! But it works for me, and can give someone looking for something similar ideas of how i done it.