They most definitely have cores prepared with the souls of the pilots mothers. Otherwise, Toji wouldn't be able to become a pilot seemingly out of the blue. But there's no reason to suggest that they used those cores in the MP-Evas. If anything, they'd use loyalists or weak minded people to facilitate dummy-plug control. Unit 01/Yui was able to reject the dummy plug outright. When Asuka is unable to start her Eva, no attempt is made to use the dummy-system, even though it had been installed and is operational at that point. This suggests that Kyoko is incompatible as well - possibly because of the nature of her split soul, leaving all the motherly/caring bits inside Unit 02. Both Kyoko and Yui went into the Eva willingly to protect their children. For the MP-Evas to work reliably, SEELE would use people who become part of the Eva to initiate Third Impact and thus don't reject control.
There is nothing to suggest that Unit-00 revieced anything more than a new paint-job. It already is a clone of Adam, a progenitor, which, I presume, is far more powerful than any other angel. The only reason that the Evas do not curb stomp any enemy is because they are artificially limited in their capabilities - limits that Unit 01 surpasses every time Shinjis life is in actual danger. Given how dangerous angelic contamination is, I don't think they'd risk it by cannibalising angel parts to "improve" Unit-00. Besides, all the other angels are inferior copies/offspring of Adam to begin with - there is nothing to gain by incorporating their parts into an Eva.
Regarding the S2 Engines, I think it's strongly implied that those of the Eva series are man-made. There is no mention of any recovery, the only angels whose corpse is relatively intact are Shamshel and Ramiel, all the other get completely destroyed. There's also the debacle with Unit 04, where they tried to install an S2-Engine built in Germany, I think. The whole idea behind mass-production is that it isn't relying on salvaged parts, being repeatable indefinitely. Relying on salvaged angel souls isn't exactly sustainable.
The MP-Evas are no more angelic than Unit 01 under dummy-plug control. If anything, they are a little slow on the uptake, just standing there while Asuka tries to tear them apart. Unit 01 immediately started taking Unit 03 apart, while the MP-Evas take some time to become active, pointing to the fact that they'd never been activated or used in combat before. They were equipped with replica-lances. They could have finished Asuka off the second they arrived, they just didn't, because the dummy system is "dumb". On the other hand, they are capable of performing the ritual to start third impact, so, maybe they aren't as dumb as they seem, but just cruel and play with their prey. Or they run on Windows 2000 and just need ten minutes to actually start up.