Tried once more and only got warmth on header pipe 3.
First I would recommend saying 'it turns over' for describing the *attempt* to start it and then say 'it fires up' when the 'turning over' results in an engine start-up (however brief the start up might last).
The engine will 'turn over' all day but 'the engine fires' leaves no confusion when you're asking for advice; just a suggestion -- it was a bit confusing (not a big deal though) but I think you meant above that you are getting her to fire up sometimes, and not simply turning over.
Here's a quick couple things to do so we can better assist you:
1) pull the spark plugs and tell us what each one looks like (is one or more plug wet with fuel? for example), and be careful to keep track of which plug came out of which cylinder so we can advise on what is happening in each cylinder based on its own spark plug.
2) put one spark plug into its spark plug cap and lay the base of the plug so it touches the metal part of the cylinder (so it's getting an electrical ground) and turn the engine over with the key on (just turn it over) and do that one by one for each cylinder. Then let us know if you saw a spark on each plug. If any plug did not spark it's important to know that.
3) if you have a volt meter, turn on the bike's key (but don't try to start it) and with the key on measure the voltage across the battery and tell us what you see (note -- make sure the + and - battery leads are hooked up to the battery when you read the voltage on it with the key on -- this is a very simple 'load test' to see how much the battery voltage drops when it's supplying power to the bike's electrical harness and fixtures).
If you do those steps it will really help advising. My guess is your plugs are fouled. And maybe the battery under load is a bit low. The bike will not run well at all if the battery is low. The symptoms sound like a low battery and fouled plugs (from all the choke use perhaps).
If you charged the battery and then you measured the voltage on it *right after* you took it off the charger, the voltage you read will be artificially high. Measure the voltage 1 hour after the charger is removed. You have a dang good battery, a Yuasa, so if you charge it right and clean them plugs you should be good to go. Those two carb-airbox boots will affect the running but are not a big enough influence to cause your symptoms -- but a low battery and fouled plug(s) are.