I would check your grounds and double check the spark plugs are right and gapped correctly. Is it getting fuel, meaning the pump is cycling? :edit:Sorry, sadly I didn't read every word of your post so I jumped the gun on the above advice. Now, are you saying you've changed the plugs AFTER this issue or before? And most likely the pumps working since the bike ran after the engine swap, so now I'm wondering ( more like hoping for you ) if it's not just a bad ground? As far as the battery is concerned, I'd make sure there's good contact on both terminals of the charger's lead ( jumper harness for the Tender ). And I don't know if it matters or not with charging, but the Tender's ground should be earthed and not connected to the negative terminal on the battery. Only the positive lead should connect to the battery