I'm not sure I quite understand what you've done with the event now, so I'll just post how it *should* look.
- op when-argument
- op in-sequence
# <list of ships>
- op true (or whatever you need the trigger to be)
- op cap-watpoint-speed
# <argument>
# 15 (or whatever)
- op invalidate-argument
# <argument>
Repeat for as many times as needed to cover all ships in the argument list, and that'll cap the speed for every single one of them.
[Edit] Oh, and as for the transports, try setting the initial escort priority (in the misc dialogue in the ships editor) to 90, 80, 70 etc. respectively as you move down the list, and then once a ship has been scanned, set its escort priority to 0 (using when-argument to achieve this for all transports while using just one event is left as an exercise for the reader).