How far off should my pulleys be from the stern and bow? My yak is only 9.5' long so do I need to put them as far back and front as possible? Will the trolley work as proficiently as possible being such a short system? As always, thanks for everyone's input and advice.

IMO, I'd mount it as close to the front and back as possible.
As far as a short system, I have a 12' and a 16' with two trollies on each side which makes each system
short and they work very well, this also gives me a lot of options when I want to anchor or use drift socks.

Yes, mount them as far forward and rearward as possible - that gives you the ability/option to get as close to parallel to the wind either upwind or downwind as possible. It will work no different even given your yak short length.

Note - take into consideration how easy/difficult it is to get access to where you are wanting to mount if you are backing the bolts with nuts (IMO absolutely necessary).

Thanks pelican. About to go rig it. Let you know how it goes.

That's actually why I started the thread, putting all the way front and back was going to be a little tough. I measured off 12" and it will be easy to get to. Will probably try to get back a bit farther than that though. But I'm not rigging it up yet. I want to put it out on the water one more time to see where she sits in the water. I figure this may save me some time and headache in the long run when it comes to something as permanent as drilling holes!

Post some pics when you get it installed!

Wrenches and sockets etc can extend your reach. I have raptors and the hatch doesnt exactly fit a grown man but i still manage to get the.washers nuts etc tight. Another tip, lubricate all stainless hardware with bar soap. Also a dab of goop on the back side of washer will hold it to the inside of the hull till you can start the nut.