hey, ill give a whirl at ur questions
1) I have a 66 coupe with a 200 and a 3 speed, when i first got the car it ran horrible. but like yours it sounded like the power was there. What i did to fix this 1. Tune up- new plugs, wires, distributor cap, rotor, and points. This gave me a decent come back in power. 2. After having the car about 3 months the timing chain oil pump ad distributor all went at the same time. 3. My cooling system was also in pretty bad condition, i replaced the radiator with a 3-row instead of the stock 2-row, water pump and heater core because the hoses on mine were cut by the previous owner due to a leak. 4. Me and my Dad had a friend who works on tranmissions for a living and he checked it out for us, my clutch was destroyed with pitts so bad they were just holes. My recomendation is find a mechanic u like and have him do an in depth checking of the car. But my car runs great now and the power is definitely restored. Hoped I answered that question.
2) I cant give u a price on the engine but i have heard from quite a lot of people that if you bolt a 289 to the 3 spd you will tear it to shreads. My friend had a friend who tried this and he blew out first gear wrecking his trany. I have also heard that the differential has be upgraded to take the power.
3) About the quarter panel try these few websites:
http://www.cjponyparts.comhttp://www.mustangdepot.comhttp://www.npdlink.com - catalog order on this site is best way to go
I have gotten all my parts to start to rebuild my car from these sites with the help of local autostores
Hope i was of help -Bill