It's hard to say. You need a more sceintific approach to the whole thing. The goal is working toward isolation of a particular issue. Also having a control or baseline from which you are starting will help everyone here help you.
It seems to me, though I am no expert, that you have communicated a few potential issues. ( jets clogged--there is more than the main hole rinning through the jets. there are holes in the sides of the jets, as well as vacuum jets in the carb body itself-- or jet too big, needle depth, float height measurement etc.
Start from the begining.
Proper jet sizes, needle depth, float height, carb sync, clean body jets, springs in carb adjustment screws, clean air filter, flat carb insulator, good o-rings, timing, valve clearances, fresh plugs. good spark, compression test.
Then- follow ed's tune up, to the "t".
Hope this is helpful. I have found myself in the same situation many times --always kick myself for not starting from the start...
MBellRacing wrote:So I've been busy...
I pulled the plugs and found that only one was consistently firing. The one that wasn't firing was MASSIVELY lean. My neighbor was luckily disassembling a Superhawk and let me take his right side ignition from him. I put it on, and LIKE A MIRACLE, it fired up and ran like a champ!!! I fixed the timing but now found that it was having some missing still in the last bit of the throttle range. I steadily increased jet size and it progressively got better and better. Now I can go full throttle and it revs quite high in 1st and seconds gear. In higher gears (higher load) it still struggles a bit and sounds lean still. The issue is that I am now on a 145 main jet with the needle in the middle slot. This sounds quite rich but its working just fine in both cylinders. I know there is a slight overbore in this engine but I feel like it is getting out of hand. Is something wrong? Could something like an air leak or something be causing me to need such fat jets?
Edit:
So I went out and pulled the plugs again. Where before the ignition change the right side plug was completely washed and clean, now the left side looks okay and the right is BLACK. Could this just be from all the old fuel that had likely filled the cylinder? Or is something else going on? What can cause this? Could a dirty filter be the culprit?