Doohan on the other hand refused to have anything to even do with him, turning down money deals just so he wouldn't have to work with Shatner on Futurama and such.
Animation lines can (and usually are) recorded separately. Doohan was on record as turning down "Futurama", IIRC, because he felt it sent up ST too much, and De Kelley had already passed away so it wasn't going to be able to include everyone anyway - but he didn't realise everyone else was fine with the script. But the ailing Doohan was also cutting down on his workload in general.
does anyone know anything personal he did to Jimmy Doohan to earn his hate?
Um... Some people suffer fools differently to others? Some people are more forgiving than others? Some people run out of patience faster? Actors have egos? Shatner was also a prominent no-show at many ST-related events not focused on him, such as the rest of the cast's separate Hollywood Star ceremonies.
Doohan and Shatner always sparkled on camera together and that's all that matters. Haven't you ever had to work with people you didn't get along with?