I just put a clutch in my 2004, and it made some similar noise for awhile. I thought I was going to have to pull it apart again & look at the pilot bearing, but it quieted down. For mine there are two pressure plates available, one is an automatic adjusting set up and the other is a plain straight forward old school type. If I remember right the auto adjust was considerably more pricey too.
You don't have a transfer case to deal with, so if you have space, tooling and reasonable mechanical skills you should be able to replace the clutch in 6 - 8 hrs without too much trouble. Your worst case scenario might be some warpage at the flywheel, which while not good would explain your noise.
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2004 Ranger 4x4, 5 speed manual, 4.0 V6
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