'88 Ford Thunderbird 5.0

My '88 Thunderbird is plucking my last nerve. Here's the story: When I bought the car the exhaust behind the converter was not connected, and I drove the car like that for about a month, and it drove good. Then one day it stalled on me, but started right back up as long as I had my foot on the gas. So I parked it. In the past few weeks I have replaced the Y-pipe and both mufflers, fuel filter, fuel lines, trans filter, air filter, plugs, wires, cap, rotor, brake master cylinder, new brake lines, and put the super expensive gas in with a fuel injector cleaner. Oh, the fuel line patch I did temporarily ruptured, so I replaced the whole line. Now the car starts right up and idles, but the idle is a little rough and makes the car shake. The more gas I give it, the harder it shakes. It seems to be ok at higher rpm's on the highway, but as soon as it downshifts the faster I am going the worse the shaking gets. I'm stumped. Also, at the same time the car started acting funny, when I put it in reverse or nuetral it locks up like I am in park. The drive gears all function properly, and shifting is smooth, but I have lost reverse and nuetral. Any help you could give would be much appreciated. I really like this car, and would hate to have to sell it because of something stupid. Thanks guys. J