I would suggest that the following items could be considered to have some relevance to the NRM.
LEV1 is already part of the NRM, so no pacer
A class 59, the first mainline foreign diesels locos and successor to the 66, one of them holds a record as well.
A class 57, showing the 'bodysnatcher' concept
The production record HST loco - pair this with project Miller, and you have a train for mainline running!
58050 the NRM designated loco
A MPV vehicle - showing how maintenance has changed compared with when the railways were built
A class 158, showing the sprinter family, and also BR's export business, (Thailand). Would contrast well with 31018 in the BR area if returned to RR Express livery
A class 170, the 'turbostar revolution', explaining how 'off the shelf' designs became common, alongside a Desiro vehicle of some sort.
As mentioned, a class 390, showing the tilt concept, alongside the APT power car that used to be at Shildon
The desiro vehicle can be used alongside the 4VEP vehicle at York, showing the change in standards passengers came to expect with privatisation.
A class 313 showing the dual voltage ideas and flexibility, as well as the BR developed PEP design.
The record breaking 442 vehicle.
A PPM
A Eurotunnel Shuttle loco - one of the powerful ones
An S Stock vehicle, the commuter story, and the 'gangwayless' vehicles.
The record breaking 91.
A DBSO vehicle, I think one of these has already been set aside - a cost reducing idea!
a MK3 vehicle, slam doors one end, auto the other, showing the idea of a refresh programme for stock
a MK4 bogie, the 140mph idea
a HTA coal hopper, coupled with the HAA MGR hopper already in the collection,
I'm sure there's lots more, that's all I could think of however