Right. Have removed and reassembled the air cleaner unit, checked all connections are good, but it wouldn't start.
Decided to try running a jumper wire from the positive terminal of the battery to the fuel pump and it started. It will continue to run when removing the jumper wire, but when I try to accelerate, it hesitates and cuts out again. The only way to restart it is to use the jumper wire again.
If I am reading that correctly it's not weird at all, makes sense.
If the fuel pump only runs when you jumper it, then you have some type electrical problem of course that the bike is not powering the fuel pump like it should. Check fuses and any/all wires and connectors where you been working. Something may be loose or unplugged.
Since it does run when pump has been jumper-ed, that pretty much eliminates anything else other than electrical to make the pump run as it should.
I think you are saying the pump only runs when jumped and bike still runs after removing the jumper? This would be normal I think for a short time.
When you run the pump you fill the carb bowls, the bike will run for awhile without a fuel pump just on the gas that is in the carbs, then of course you run out of gas because the pump is not pumping in more.
If the above is correct in your case then that is why
"when I try to accelerate, it hesitates and cuts out again. The only way to restart it is to use the jumper wire again."
Your out of gas again because the pump is not running.
It's kinda amazing how long a bike can run on just full carb bowls really without a pump working.
When I want to run an engine out of gas it seems to take forever just sitting there idling and revving it sometimes.
With my 1100 when it sits for a long time like months or so 1 o-ring will dry and leak gas for awhile next time I try to run it. I just went through that again after having let it sit near a year now.
Once the O-ring is wet for awhile it stops leaking and all is fine.
SO, wanting to see how the bike ran after sitting the year I turned on the petcock till the bowls are full and 0-ring just starts to leak, then turn off petcock. As the bike tries to run out of gas as the bowls get empty I just turn on the gas again for a minute to refill the bowls.
I can ride a really long ways on just the fuel in the carb bowls! Once I had the O-ring leak slowed to just a bit of dripping I took the 1100 out and rode about 40 miles or so. I turn on the fuel to fill carb bowls a minute or less then turn back off, I ride a long ways before the 1100 starts to act low on fuel then I just turn on fuel till she smooths out again then turn fuel back off again. A nice thing about having a manual petcock I can reach easy.
I mention that because you can do the same thing with the jumper wire to the fuel pump. Connect it to run pump and fill the carb bowls then remove it. When bike starts to sputter, or hesitates when opening the throttle connect the jumper wire again. I'd not ride that way of course, but for testing purposes you should be able to keep the bike running as long as you want that way.
That would verify the only problem is bike does not power the fuel pump when running like it should after started.
As for the leaky O-ring on my 1100 I mentioned, it don't leak a drop now!
I just had to get it wet and warmed up to riding temps for awhile.