I plan to get started cutting into the pile of stickered timber in my yard in the near future but one question has consistantly bothered my brain:

The timbers are roughsawn and therefore will likely vary in width/depth from piece to piece. Where a girt or tie joins to the posts I expect to have to adjust either their length or plane the area of the posts where the timbers join to a consistant dimension.

Does anyone have any advice on the best way to go about this?

Ok, so I've come to the realization that I'll have to cut a seat to a consistant mark so that all of the girts and ties can be the same length. I had planned on doing an eased haunch up to this point, partially for aesthetics and to keep stress off of the tenon. Is it practical or possible to still use this joint?

Bandsawn or circle saw? What are the differences you see from end to end, under or over sized by how much, bows or twists/wind?

Look into square rule, snap line square rule, and scribe.
When scribing you don't have to deal with housings and reductions, unless you're seeking more bearing surface for a tie beam. It is nice to smooth off any crown in the faces of timber when using PLS.

A very basic explanation of snapping lines on a timber for plumb line scribe and/or snap line square rule.
https://www.youtube.com/watch?v=Iz3R4IfSMtE

One end of a brace with a snapped line.
https://www.youtube.com/watch?v=1UPFAFwG3ts

The timbers are circular sawn..I havn't inspected many to see what kind of movement has happened since I stickered them. I need to learn more about scribe rule or snap line but can't find much explanation. Is snap line just snapping a straight line up the timber and doing all of your mortises off of that instead of a face?

Basicly, the snap line is where all your info is based off.

If the timber is true, square, and straight you can easily use the edge. It isn't often you get all aspect fall together with rough sawn stock.

My understanding of scribe rule is that I will have to place the adjoing timber ontop of the piece it's being joined to and then plumb down. I'm doing the joinery in my barn and expect this to be cumbersome.

I'm not too concerned about the posts that face the outside but the ones that are completely inside.. I wonder how to do the ties most efficiently. Will I be able to make all of the ties all the same length with scribe rule?

Square rule sounds like the solution. Read Jack Sobon's two books for a description.

We are finishing up a PLS frame, yet the rafters are almost stick built quality, very simple fastened to a ridge plank with a simple plumb cut, the seats are like lapped rafter seats with no tails. Removed most of the joinery in the rafter system.