Ok lets see who can figure out what I messed up!
First let me explain the changes I have made to the bike:
Ok, so I bought a 96 engine for my 87 savage. I really wanted the five speed. Also my 87 was clunking hard when I shut it down so I wanted a post 95 engine so it would have the torque limiter assembly in the starter idle gear. (Turns out on my 87 the one way starter clutch was froze up and siezed to the hub of the starter driven gear! But that's another story) However, it would not be just an easy swap out. The 96 engine's right crank half had a hairline crack in the bottom and leaked enough so that I couldn't run it as is. Therefore I needed to completly disassemble both engines so I could install the right crankcase half from my 87 engine on the 96 engine.
I used Hondabond HT to seal the two crank halves and put in new gaskets and cleaned everything good while it was apart. Also I needed to swap Magneto rotors to retain my stock 87 ignition. Thanks to forum member Dave I was able to borrow his rotor puller tool and saved about $50! After the engine was back together it was time for the Dyna muffler swap I've been wanting to do. Thanks to Serowbots awesome post on Dyna mufflers it sure makes the swap easier to tackle. I ended up getting a 10 degree offset adapter pipe made up at my local exhaust shop to connect the header to the muffler.
Next I had to swap carburetors. When I got the 87 savage, it had sat in a barn in New Hampshire for ten years and the carb was a mess. The pilot screw was froze and the the slot on the top of the screw was stripped. The float and bowl were covered in green slime and just reeked. So to save time getting the bike on the road I picked up a carb on ebay and have run that up until now. That being said, I wanted to put the stock carb back in the bike because it came stock with a 155 main jet which I figured would be better with the Dyna muffler. Also the one I have been running is a California model and the pilot air jets are different so I wanted to get back to the original carburetor. I ended up drilling a small hole in the pilot screw and using an easy out to back it out. then I thouroughly cleaned and reassembled the carb.
Now let me explain the way the bike ran when I finally got it all back together.
Fully charged newer AGM battery.
Fresh gas
Clean plug with good spark
Choked it and hit the starter button, It fired immediately, but was running roughly. It absolutely would not idle, but, I could keep it running by constantly working the throttle. Every time I tried to get an idle it stalled and backfired loudly. When it would run it was backfiring, and misfiring and very rough. The closest I could get to an idle was about 1700-1800rpms and very very rough and all over the place. If I opened it up it would rev up and ran slightly better, but, still didn't feel right. I had a fan on it the whole time I was working on it running to keep from overheating. Clue: It ran as though it were lean trying to die and backfiring, but, it was puffing black smoke!
Now for total disclosure, I have found the problem!
Let's hear some guesses and ideas. You guys are always so good at helping newbs with their bike issues that when I finally figured out what I had done my first thought was whether any of the forum members will be able to diagnose by reading my description. Can't wait to read replies.