Hi Daytrip,
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.