Is there any reason the PPT line couldn't be electrified? Is the headroom that tight? They managed to get overhead lines into the tunnels to Greystones, which seem pretty tight. To my casual observation the PPT seems luxurious by comparison.
Regarding the Interconnector/DART Underground, I'd rather see it left out of the plan than done wrong. I'm hopeful that we'll eventually get a government who actually care about rail and will resurrect it. If a budget interconnector was built on the cheap and wasn't up to spec, we'd probably never get another chance to fix it.