It's never too late to start composting in the run. There is plenty of time left this summer to toss in grass clippings, etc... and get things going good. It's just basically a cold composting system, so it just needs time to sit and decompose. The chickens scratching and pecking all the litter speeds up the process. If you want, add watering to the chicken run to keep things moist, which will also speed up the decomposition process.
I estimate that it takes about six months for my chicken run litter to turn into black gold compost. Obviously, in Minnesota, we don't have 6 months left of non-snow weather. So you can either harvest some of the chicken run litter in the late fall and dump it into your garden to winter over, or you can let it sit in the run and continue to compost under the snow and see what it looks like next spring.
Last fall, my chicken run litter was about 18 inches high after I added all my leaves from the yard. Over winter, that continued to break down and this spring it was about 12 inches deep. Lots of good composting occurred over winter.
Most of my chicken run compost is made up of grass clippings and leaves. Yes, I do toss in my spent coop bedding with chicken poo, but most of my compost is from grass and leaves. Knowing that, this spring I harvested my chicken run compost from over winter and added it directly to my gardens. I have so much organics in my compost compared to the small amount of chicken poo in the litter, that I would not worry about using it before it had aged for 6 months.
I don't use a poop board or anything like that, so I don't have concentrated chicken poo to put into the garden. I use deep bedding in the coop, so even my spent bedding in the spring has relatively little poo in the litter compared to the bedding I use. I toss all the coop bedding into the chicken run to age and compost because the dry bedding does not start composting until it is outside and exposed to weather.
I don't know why you would want to remove the pinecones, but I use my cement mixer compost sifter to sift my compost and it automatically rejects any large bits and chunks bigger than my sifting screen. I typically toss my rejected too big litter back into the chicken run to continue composting. Eventually, everything will decompose, even in Minnesota.
