When we, as students, took the workshop at Hancock Shaker Village with Jack Sobon, we build a shed/barn/house/cabin similar to the one in his book. It was mostly pine, but some fir beams also.
We started with the floor joists, then the sills, then the posts, tie beams, plates and finished with rafters.
I'm not sure if he had us start with joists to that we could make our mistakes where these joints wouldn't be seen, or because that's the way he likes to do it.
But we measured all the joist ends and used the smallest of the joists as the width for all the joist ends and the joist pockets in the sills. By doing this the joist were all the same size and inter-changeable and the largest they could be. More than the standard 1/2" reduction for sizing the ends. This also makes the joists stronger. Using this larger than 3 1/2" size we centered the pockets on the 2' mark and cut them to this larger new width.
As we were cutting and erecting this frame in one week there was very little time for shrinkage of the timbers.
This measuring to find the smallest and then using that size as a standard for one shed is the procedure I use now. Therefore you have to have all your joists on hand before you layout and cut your joist pockets on your sills.
My advice would be to follow a similar procedure. But that's just the way I do it.
Good luck with your project. Jim