|Perhaps the type of formula is having an effect, I'm not denying that. Just saying that increased staining is pretty typical as babies get older and start on formula or solids.
Staining is pretty normal, sunning for longer periods might help. I remember a few diapers that had bad staining that just wouldn't come out. I was getting them ready to sell so hung them outside again as a last ditch effort. It was winter so I wasn't expecting much and just ended up forgetting about them there for something like a week. When I got them off the line, the stains were almost all gone. Sometimes leaving them out for a long time can help. Lemon juice is also supposed to help boost the powers of the sun...
Poopy odor sounds to me like what you said about them not getting clean enough (as opposed to build-up for example). How much detergent are you using? Do you think the wash water is hot enough? If it is the formula maybe it has tougher kinds of oils to wash out and you need either hotter water or more detergent? Especially if you've been trying to avoid build-up by using a reduced amount of detergent.
As for the detergent itself, I know ME recomeds it but according to at least one diaper detergent chart - http://www.pinstripesandpolkadots.com/detergentchoices.htm -
it's not a good choice. It's not considered strong enough for diapers plus it has a host of problematic additives. Maybe it was ok before the new formula but if this one is tougher to wash out, maybe you need a stronger detergent?
Your routine itself doesn't sound all that problematic but maybe try using a wet pail? Don't know how true it is but some say that wet pails can increase odor problems (of course others say the exact opposite so it's obviously not an exact science!). Worth a shot, at the very least it'll simplify your routine. Although if the stains really really bother you then a wet pail is probably what's best at reducing those...