1. Intern year. I'm actually kind of against the whole trend of people taking it in MS-4 to get it out of the way if you're going into IM because basically intern year = studying for the exam. There are tons of things on the actual test that come up on the wards, and I felt like I would have to study a lot more to perform at the same standard if I were to take it before intern year. Also, most programs will give you the 2 days off, so why work more? Also look into whether your residency will cover the cost of Step 3. It's a no-brainer if they pay for it.
ps. don't sweat the surgery/obgyn/peds stuff. It's like 30% of the actual exam and you can cram that before the actual test easily
2. UWorld (qbank and CCS) is sufficient. You can read through MTB if you want but I found it not that helpful.
3. Tons of hearsay (because no one is a fellowship director or can speak for fellowship directors). From what 3rd years and a few of our fellowship mentors tell me, if you're going into really competitive programs in cards/GI/pulm/hemeonc they'll comment about your Step 3 if it's abnormally high or low, but the ones who matched into the "less competitive" fellowship fields say it absolutely does not matter. The consensus from the people I spoke to seems to be as long as you're not more than 1 standard deviation below average ("abnormally low"), you will be fine.