Lets's briefly review where we are right now. The injectors are clean and the MAF appears to be working properly. there is good spark. Something is not right about the #3 air inlet and the engine still runs like crap.
This thread is now one of the longest in the history of Motobrick. To go back and see what all has been done and seen so far is rather intimidating. Perhaps as a public service you could list all the stuff you have checked and/or replaced so far. Things like the fuel pump, fuel filter, fuel lines, fuel pressure regulator. Etc.
One thing I wonder about is the plug wires, specifically for the #2 and #3 cylinders. When they are reversed the engine will start and run, but like crap. This is something that has happened in the past on several other bikes. It happens because the #3 lead is longer than the #2 so it can be folded back. A new owner sees this and gets the wires reversed and the bike runs like shit. This may be your problem.
Unfortunatly,the leads are in the right place. The longest lead is on no.3,shortest,no 2,and middle length lead,no 1, but yes, I can see how this would confuse some people. The pump is new,as is the strainer on it,as are the inner tank pipes with no leaks.
The injectors have been sent off and cleaned and are all within 2.3%of each other on the flow rate chart. The pump pumps as it should, as I took the pipe off of the fuel bar and fired it into a can.
The rubber pump holder is new, too,so no contamination. The Sparks are blue and fat,
Havnt changed the regulator as I'm guessing it's working,as fuel is being fired out pretty well. The plugs are new,the crank breather z pipe appears not to leak and the MAF seems ok.Its a pig to start,the choke dosnt really work until the bikes warm,then it goes to 2000 reeves,half open,4000 revs fully open. I'm using new clean fuel.I can only guess an air leak,not checked the valves yet.