New Engine Idles Rough

[LSUMurse]

I took out my 307 and put a new GM 350 crate engine in. It has the Holley aftermarket throttle body. I did the initial break in and have had it out on the freeway a few times. It initially had some issues with rough running to the point that it would not stay running unless it was revved up. That was cured with finding a vacuum leak. It was miss firing in high RPM's. That was cured with a timing adjustment (it was at 16* BTDC, now it's at 9*. I guess I didn't tighten the bolt enough and it walked).

The thing I can't seem to figure out is the rough running in idle. I've cranked up the idle speed to 1100 when in nuetral to try to compensate. The idle speed when I shift into gear will drop down to about 600. This seems too low to me, but 1100 in neutral seems high.

It smells like it's running rich, but when I try to lean it out it runs rougher. I do have exhaust leaks on both sides between the exhaust manifold and pipes. I assumed this was due to me not disconnecting the manifolds from the pipes during the swap, however it does spit out some black sooty stuff from the exhaust now, something it never has done before.

Link to the system I bought:
http://www.jegs.com/i/Chevrolet-Perf...353K3/10002/-1

I also replaced the starter, water pump, and alternator.

I have exhausted my knowledge base on what to try next. Any suggestions would be appreciated.