I'm not convinced that footbridges with lifts are required if some of the loops are lengthened to incorporate the platforms. These dates no great need for parcels offices, goods offices, milk docks etc so should be plenty of room to install footbridges served by long ramps (ramps are lot cheaper than lifts, especially if they traverse a cutting)
Most of these are semi-rural stations with quite a wide catchment area, but really these stations need to be able to handle full length trains (something like 240-270m depending on what length coaches next generation trains will use), so lengthening platforms might allow footbridges to be in new location. I might go further and suggest platforms should be about 30m longer than trains to stop some of the over cautious approaches as it wont matter if it finally stops about 20m further along, and would more braking leeway. Even saving 10 seconds per stop is 2-3 minutes overall. My memory might be fuzzy, but I'm sure the Southern extended some platforms to about 15-16 carriage lengths in 1930s. Therefore some platforms might already be nearer 300m
Having got longer loops (or even a token number of dynamic loops), need to be able to enter and exit them at a decent speed, but that actually makes the job of installing the long turnout easier, because doing it on the plain single line beyond the current loop. If any existing ones are in good condition probably possible to break them into sections for reassembly elsewhere. These days big cranes mean these can often be part assembled clear of the running lines.
As we nowadays have 110mph gangwayed EMUs, could easily have 110mph bi-modes on the line. I know the 159s are not yet life expired, but there are many other lines where there is a serious shortage of rolling stock, easy to cascade in old days, but more complicated when a leaseCo is involved. So I would also be looking to get the longer sections to this higher speed limit. With the higher speed loop approaches should be looking to cut station-station running times.
Regarding electrification. Stringing the wires up Wilton - Basingstoke - Reading is a logical progression (and third rail would be better than diesel if stupid no extension rule didn't exist). Not convinced that doing the section onto Exeter makes sense at current time.