The two MP36s were black sheep as they had their own maintenance needs compared to the rest of the fleet, and at the time, the MBTA wanted more but couldn't get any (there were none on the secondary market, and MPI couldn't build any more as they were not EPA Tier 3 compliant).
MP40s were an option in the first round of bidding as they were made EPA Tier 3 compliant, but they did not fit the MBTA's needs due to weight. The MBTA operates at 79mph on the corridor and the MP40s would put too much wear on the track due to the weight. The only agency that operated them at the time (GO Transit) did not operate at such speeds with them. There was an option to reduce the size of the fuel tank to reduce weight, but the MBTA did not like that option. The inital winner of the first round of bidding was Vossloh Espana (Vossloh's former Spanish arm) who would have built an Americanized version of the Vossloh (now Stadler) Euro 3000, but they pulled out when they were not able to get a waiver for the Buy American Act. After a second round of bidding, that's when the MPI HSP-46 proposal won.
(In hindsight, it was good that we never got the Vossloh units as they would possibly be in limbo at this point for support as Vossloh has pulled out of the business; most of their rail products have been sold off (ie the Euro 3000 is now a Stadler product), and the construction of remaining Vossloh branded locomotive products are now built by CRRC)
The F40PH-3C rebuild program should have been done earlier, but the problem was that the locomotives probably couldn't have been rotated out at a sufficient pace at the time to make any real progress as the GP40MC top deck overhauls were being done at the time. The delivery of the HSP-46s helped immensely to free up older locomotives for overhaul.
