I have now checked just about every connection that we could have possibly messed with (vacuum lines, distributor wires...) and everything there seems to be connected just fine. My new diagnosis is that the timing is off. The exhaust stutters, the engine shakes (a lot), between about 500 and 1000 rpms the smoke coming out the exhaust is gray, up to 2000 (which is the highest I could rev it before it cuts out all together) there is a lot of black smoke. I think that's all the symptoms. I am going to check the timing later today and if that doesn't fix it....