Clark Canyon Reservoir at the top of the Beaverhead in the SW corner and Henry's Lake, more towards West Yellowstone would be good bets. To get away from the crowds, try Cliff and Wade Lakes off the Madison, below Ennis (spectacular scenary) The Anaconda settling ponds just off I-90 near Anaconda of course have had monster fish in them.
Pick up Steve Probasco's or Greg Thomas' books on Montana...pretty helpful. Or, just send RT a plane ticket and he can meet you in Missoula!
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Chasing old rags 500 miles from home.