1. An initial yellow-orange flame when you first crack the regulator is normal (assuming your new stove behaves the same as a Whisperlite). To minimize issues with this initial flare up, when I'm first starting it, after priming flame has mostly died down , I always just crack the regulator for as short a time as possible and immediately close it again. This usually results in a manageable yellow-orange flame that dies down in a couple of seconds. I repeat this 'burping' process once or twice, and usually the second or so time I burp it, the flame comes out blue. People seem to have problems with this initial step. The initial flame is yellow orange, and they seem to think if they open the regulator MORE that it will improve things. That's when fireballs erupt. Also, the initial flare up is worse if you don't prime the stove well enough, but it doesn't really sound like that's the problem here. FYI, I've always found that it's better to over-prime than under-prime. If you over-prime, you get a bit more of the yellow orange flame while you're priming, but I always found that completely manageable, as long as I had the wind screen set up. On the other hand, if you under-prime, you're definitely going to get a substantial flare up when you first burp the regulator, and it'll take quite a few more burps before your flame is blue, because the stove won't be up to temperature yet. Again, this is where I see people have problems/fireballs.
2. I always removed the pump from my fuel bottle. I found the plunger would sometimes extend, making it vulnerable to breaking. Actually, for one or two trips I left the pump in the fuel bottle, having seen others do it, and on one occasion I broke a chunk off. It was still serviceable, but I thought it riskier to keep the pump in the bottle than to detach it and keep it separate, usually near the top of my pack where it was less likely to be damaged. It takes almost no time to put the pump in, so I didn't think that time savings was worth the increased risk of damage to such a critical piece of gear.
On the whisperlight, if the plunger move up it means the check valves arent seated.
I dont have my whisperlight handy but on my Dragonfly pump, the check valve is in the tip of the pump. Its just a rubber ball held in with a spring. In order to understand how the pump works there are some basics to understand. The fuel pump actually pumps air into the fuel bottle rather than fuel. The pump seal is a leather cup attached to the plunger. The leather is formed in a cup so that when its lifted up it lets air past the leather seal and into the cylinder that the plunger slides in. When the plunger is pushed down the rim of the leather cup expands and seals against the cylinder walls which causes the air in the cylinder to pressurize. The only place it can escape is out a hole in the bottom of the cylinder. The hole is blocked from the outside of the cylinder with a rubber like ball that is made of material that is not impacted by the fuel. The ball is held in place against the hole with a spring. the other side of the check valve is vented to the inside of the fuel bottle through a tube. When the pressure in the cylinder exceeds the pressure in the fuel bottle, the rubber ball will lift the spring and will flow into the fuel bottle until the pump hits the bottom of the cylinder. When the plunger is lifted, the leather cups outer diameter gets smaller and the rubber ball is pushed back into the hole by the spring sealing the pressure in the tank from escaping out back through the pump cylinder.
If the ball or its seat is plugged with debris it may not seat and then pressure in the tank will push either air or fuel back up the pump cylinder and out the pump and may lift the pump rod up (sometimes it doesn't ) and will leak all over the place. On the Dragonfly, its obvious when the check ball lifts the spring. If the plunger is pushed down when its not in the fuel bottle it will build up resistance and then release it and if you put the finger on the end of the tube that goes in the tank you will feel a puff if air.
I had one of the defective Dragonfly pumps long ago, it worked but was on its way out. I had another stove and set it aside. While doing an AT section hike a year or so later, with my pocket rocket for cooking I found a Dragonfly pump abandoned in shelter. It looked like someone had tried to pump used motor oil through it. It was gummy. I threw it in the pack and at some point when I got home I cleaned it up thoroughly by disassembling it and soaking it in white gas and didnt even need to replace the seals and its the one I still use on the rare occasions when I use it for larger group cooking.
The defective dragonfly pumps was a black mark on MSR, they came out with a newer design that cured the defect but they refused to give free replacements yet would gladly sell the new design.