Can you reach down into the engine with a grabber to get the feeler gauge?
I took my flywheel off last year and it was pretty easy to do. After removing the bolt that holds it on. I found an appropriately sized metric bolt (actually the rear axle bolt of my friend's KLX250) and screwed it into the center of the flywheel. With the bike in 6th gear I turned the bolt until the flywheel popped off.
I understand the changes you are making. It may be too late for this but I would caution you to not change too many things at once. After setting the valves it would be good to know what if anything has changed in the way it runs.
If the tight valves have allowed the head to be damaged, you may want to hold off on farkling the bike.