It could be one of many, many things. I highly doubt a bolt inside the transmission would be the cause.
Check the exhaust. Sometimes as the engine revvs down between shifting, it can cause a vibration in the exhaust that usually doesn't happen. Mine does this, and makes noise, when I let off slightly at highway speed. I recommend laying down and kicking the exhaust system, or pushing it with your foot. It shouldn't move any, if at all. If it does, you may have a broken hanger.
Check the transmission cross-member. This is the metal piece that is right under the seats that crosses between frame rails. It literally holds the transmission up, and has 8 bolts altogether. 3 on each end and two holding the trans on.
Finally, have someone drive by while you listen from the curb. A lot of times what you hear sounds different from outside, and may help you track it down.
Finally, post back on here and let us know what you find!!!
The Black Beast 5.0
Better to Have Horsepower and not Need it, than to Need it and not Have it!
2000 Ranger Sport - 5.0L V8 - 8.8 LS rear