man i do hate rufus, but you could won that imo, cuz he was doing unsafe shit/gimmicks (ie. 3 divekicks in a row? and mesiah after mesiah? cmon), i believe you just need more exp in that MU, i dont find it THAT difficult tbh (to me blanka and viper are more diff and Rufus to me is at the gouki´s level of difficulty, doesnt mean that is free either lol).
Against dive kicks try to late tech as much as you can, if you block one and if you have meter wait a little to see what´s going to do next, if he is doing another divekick do an EX sbk, he wasnt frame trapping you with st.lk, cl.mp so teching wont do any harm, if rufus jumps st.hp is your main AA, followed by max range cr.hk and st.mk, be careful with delayed divekicks tho, in this case he wasnt doing that, good rufus can mess with your spacing a lot with delayed divekicks. In my experience neutral jumping hk/hp is a good tool to use against air to air, do not overuse it tho (even air throw is a good AA, many rufus forget about this).
If rufus has meter bait the mesiah, they are slow as hell safe jumping them is not hard at all, f.throw, walk, j.hk will do as a easy safe jump. I use U1 in this MU, better damage after a EX legs, punish to his mesiah´s followups (including mesiah fadc) and cr.hp, his sweep is punishable with super same goes for EX galactic tornado. Another tip against his normal GT, he is -1 on block but mk super wont punish this, in the other hand he “cant” continue any pressure, but he can use this opportunity to bait some punish and activate mesiah, in other words you have to look for patterns, some rufus wont attack you after normal GT, but other will, punish accordingly.
If i have not say this is just because is pretty obvious: DO NOT JUMP WHEN HE GETS ULTRA, some rufus love to spam j.hk fishing for a jump, punish it on landing. Oh and remember the second kick of his target combo whiffs against crouching chun, cr.lk or cr.lp BnB will do.
Against happy backdashers i use the following OS: f.throw, dashx2, meaty cr.lp, st.lp+hp (hold back while doing this), in block you will see 2 jabs chaining, but in whiff st.hp tag rufus backdash, and if he does wake up mesiah you can block it. Why not OS sweep? because it loses to wake up mesiah ;_;.
i think that´s something you can use against rufus, you are free to disagree with this /disclaimer