Fundamental point is that the PEPs were 75mph inner suburban stock, intended for shorter journeys. The Great Northern electrification needed something swifter and better suited to journeys out to the likes of Stevenage, Hitchin and Royston and able to get through the two-track section across Welwyn Viaduct nice and quick, hence the 90mph 312, a souped-up 310, based on what was considered a pretty robust bit of kit.
Surely the 312s were just updated (rather than souped-up) 310s. The 310s were designed for the London outer suburban services when the WCML electrification reached Euston. Previously, a few of the NW class 304s covered, but they were 75mph stock so were difficult to accomodate with LHCS stock paths. The 310s had an acceleration rate of 1.1mph/s/s to a 90mph max, which was a compromise between the 1.3-1.4mph/s/s of the 304s and the typical 0.8mph/s/s of a class 81-86 + 9 express.
When the GE services were expanded in the mid '70s there was a need to interleave the outers with the Clactons and the class 47 + 9 Norwich expresses. The speeds between Shenfield and London weren't an issue for the 75mph stock but beyond Shenfield, there was plenty of class 309 and Class 47 LHCS running at speeeds up to 100mph. The 310/312 design's 90mph with 1.1mph/s/s was a good compromise for running in with the class 309s which typically in a 2+4+4 set could attain 0.9mph/s/s on their way to 100mph.*
The main difference between the two types was that by the time the 312s were made, the safety rules meant that flat widscreens replaced the wrap-around ones originally put on the 310s.
* In the '60s when the 309s were introduced, the service between Shenfield and Chelmsford at under 8 minutes start to stop for the 9.5 miles was the fastest in the world. A clear indicator of the gains brought by 25kV electrification.
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They were not compatible. The electrical and air connections are in the centre of a 312 which isn't gangwayed but at the side of the gangwayed 309 in common with other gangwayed stock.
The different acceleration rates are irrelevant. 310s and 312s were coupled together. Besides a 4 car 312 was rated at 1080 hp and a 4 car 399 1128 hp - surely not too different ?
Other than when they started extending the 2-car 309/1s with ex-DMU and LHCS coaches, I've never seen a 309 coupled to anything but other 309s. They were quite conventional EMUs with GEC DC motors fed from transformers via rectifiers but their performance always seemed so much better than the 4-CIGs etc. as the ac power supply wasn't compromised like the 750VDC 3rd rail supply was (and still is).