I was recently reading a ride report from someone who recently traversed the west section of the Iron Horse State Park (John Wayne Pioneer Trail) from Rattlesnake Lake to just east of Hyak for a biking and fly-fishing trip. It's not every day that people write up detailed reports about the trail. Russ and Laura did a great job documenting their trip. I hope someday I can meet "Steve," who they mention has researched and written quite a bit about the JWPT. 

Bikefishing on the Iron Horse Trail with Russ and Laura - pathlesstraveled.com

Bikefishing on the Iron Horse Trail with Russ and Laura - pathlesstraveled.com

This write-up led me to bikingbis.com which talks about tunnel repairs being done in Iron Horse State Park by WA State Parks...

Contractors are working to repair two tunnels on the John Wayne Pioneer Trail that have been closed since 2009 when inspectors found falling debris hazards inside of them. The two former railroad tunnels — Numbers 48 and 49 on the old Chicago-Milwaukee-St. Paul-Pacific Railroad, commonly known as the Milwaukee Road — are located east of Snoqualmie Pass between Hyak and Easton.
— http://www.bikingbis.com/2013/06/13/state-repairing-2-more-tunnels-on-john-wayne-pioneer-rail-trail-2-others-still-closed/

Tunnels 48 and 49 will reopen soon (July 2013?) while tunnels 46 and 47 and not being repaired. A quick visit to the State Park Website explains that, what the tunnels are still closed, riders can pass through them if they sign a waiver. 


Public safety notifications for Tunnels 46 and 47 (near Thorp) if you enter these tunnels you do so at your own risk. Prior to entering the tunnels visitors are required to fill out a waiver form and place it in the drop box located at the entrance of each tunnel.
— http://parks.wa.gov/parks/?selectedpark=Iron Horse&subject=all

Without the waiver it is a 15-mile detour around the tunnels using local roads, which would mean you skip the Yakima river canyon between Thorpe and Cle Elum. I think I know the option we will be using. }B^) 

UPDATE (12 July 2012): Tunnels 48/49 are OPEN! Also, the Rails-to-Trails Conservancy did a great piece on the tunnel repairs last December, which I evidently missed.