That is a very long laundry list of stuff to do. I would try and not try and do all them at once, cause you won't know what it was that you did that had a specific effect on the bike. Basically, you probably aren't going to get EVERYTHING exactly right the first time. It is possible but not likely. With pods and no baffles however I think it is safe to say that you are running lean. However, what is the history of the bike, did you mod the airbox and exhaust or was it the previous owner. It might be jetted properly but you missed something during the cleaning. As you can see there are many variables, unfortunately that is probably going to mean you might have to take them on and off more than once. What are your jet sizes, are they stock? If not what size are they? Seems like from what you have said you have done somewhat thorough job on the electrics, but not as extensive with the carbs.
Commonly a 1/8" drill bit is used for bench syncing. All this will do is sync each slide so they are all at the same level to start with. The other part of bench syncing comes from setting them at that level where you still have a range of motion both ways to allow adjustment with the idle screw when it is running. For example, I can adjust all them with the 1/8" bit and get them all synced at that level WITH the idle screw maxed or close to max in one direction. They would all be "synced" but would not be able to be adjusted with the idle screw properly, if that makes any sense.
The emulsifier tubes are just pressed in, so they have to be pressed out. It should not take a lot of force to do this and if it does there is something wrong. The little flange opening where the needle goes into the emulsifer tube is thin, so you want to avoid pounding it out with something metal, or maybe you could get it out with a proper sized punch. Basically don't be silly and use a screwdriver or something cause you are going to mangle it. I use wooden dowels, gently.
The emulsifier tube is a separate circuit from the idle circuit though, so your symptoms are not necessarily indicative of that being the problem, but that could still require cleaning. From what I read you can't start the bike at all? Basically it sounds like you need to go through those carbs properly, it can be a pain to do but people here will help you or answer any questions you might have.
I just finished this set of carbs and here is just what kind of visible effects can come from a bike sitting for a long time. This is just what you can see, now imagine all the little passageways with similar problems.
