Mine does that clunking sound too so I guess it's pretty normal. If you think about how fast it shifts and goes into gear it would be like taking a t-5 and side stepping the clutch between gears.
Mine runs hot also and I have a tranny cooler.
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James Cox
nochevy@hotmail.com
1991 Mustang LX
12.565 @109.38mph 1.764 60ft