Please Help....

I have a 93 AWD Aerostar extended minivan that has about 155,000 on it. The Trans was rebuilt at around 30,000 from Ford on a warranty from the previous
Getting to my problem, recently I have noticed that only in third gear I get the jerking (feels like jerking from being in the wrong gear while driving a manual) when I step on the gas to pass or climbing hills etc. First and second do not have this phenomenon while in drive or manually shifting with the lever. I have noticed the occasional clunk when I take my foot off the gas and then depress again but this doesn't happen very often.
I have checked the fluid, levels are ok but the fluid smells a tad burnt. I have read that it's not a great idea to change fluid on a tranny that has high mileage especially if they haven't been routinely maintained. My final question is should I change the fluid/filter and if so will it do anything.
This last month has been a very interesting one, new plugs, new muffler, new brakes all the way around, new shocks all the way around, and a new fun fun!!! I can't begin to imagine how much I would paid if I didn't do the work myself. Boy are minivans fun to work on!
Any help or info would be greatly appreciated!!!
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