Just build them like the Airo sets. ALC, then a business class with PAN, transformer, rectifier, inverters, batteries, powered trucks, and power cabling to loco. In stations with CAT the PAN is up, diesel shut off, CAT providing HEP thru inverters and charging batteries. Leaving station on CAT, start diesel and when CAT ends diesel goes to max power with batteries helping to obtain 8 axel acceleration.
Once reaching max track speed then use whatever portion of diesel power needed to maintain max track speed and charge batteries with left over power. If batteries not fully charged when slowing regeneration also helps charge the batteries. At station stops either diesel of CAT finish charging batteries.
Not sure if west side connection CAT is energized but use it to maintain max track speeds to end of CAT at about 48th street. If CAT is extended up west side all the better. Using third rail pick ups will limit HP that can be supplied for running as maximum of 4 shoes not enough for a full ~8000JP available with CAT. That also limits the Amtrak trains to MNRR, NYP, and LIRR if problems of pickup shoes not getting knocked off as sometimes happens changing from underrunning to over running 3rd rail.
This Airo type operation is much more flexible being able to use present CAT limits BOS, NYP WASH, & Harrisburg,
already proposed future CAT - Wooster, Springfieeld. SEPTA & NJ Transit routes