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So Just a heads up this is my first post and I'm just looking for some maintenance help with my lovely 2005 Honda Civic EX Special Edition.

Quick info about my car: Originally my sisters she drove it for a few years and took relatively good care of it. Aside from a few battery deaths there have been no issues with the cars mechanics/engine. I don't really know **** about cars except how to change the oil, tires, and gas. I also look like I know what I am doing when I stare at the engine, but I don't.

I have two main questions/issues with my Civic that you guys would probably know, (better than my mechanic). One is simple-ish, the other a real mechanical issue.

1. I just hit 89,000 miles, and I have heard 90,000 is the time to do a full maintenance checkup. What do you guys recommended I do, and what should be the cost? (additional info below)
a. I recently got new spark plugs and a timing belt (due to the issue below)
b. My rotors need replacing (I get a bit of a jerk and vibration in my steering wheel when I brake fast when driving fast), my mechanic told me it is the rotors.
c. I put in some new brake pads, and calipers(only in rear) last year (12k miles) ago.
d. It is an automatic.
e. I am not a racer or Modder, I drive fast-ish but not fast compared to some people, and the car is mostly stock.
f. I live in Connecticut, which means snow in winter and heat in summer.
g. I am probably going to get new tires soon. Any recommendations on brand?

2. My recent engine issue: less then a month ago I started feeling a jumping/stutter in the acceleration when I was driving; it felt as if the cylinder weren't working together. It was a lot stronger at higher mph. I originally thought it was just bad gas, as the issue went away for two days after I put some premium in it. However, it came back and the check engine light came on. So I went a mechanic. He plugged his computer in and said I had valves 1, 2, and 3 misfiring. So he replaced the sparkplugs and the timing belt. All was good until a month later when it started again, this time I felt as if the RPM was lower than normal it would stay right below 2k when it usually was 2.5k. Went back to the mechanic, same issue valves 1-3 misfiring. He opened her up checked the spark plugs and didn't know what was wrong. So we took her for a drive and everything was fine again. That is where I am now.
I don't want this thing to come back and maybe cause some real damage next time, I want to try to find out what the issue is and solve it. Any ideas what this could be?

Also anyone have a good way to cover up scratches, and cracks in the body? I have a dark grey 05.

Thank you ahead of time.