Lined Valet Tray / wrinkling and dye to thread transfer

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Hello All - I have been making some prototype valet trays which I am fairly satisfied with however I am coming across two issues:

1.  The glued lining wrinkles too much when bending and snapping together the corners.  Is there any way to prevent this from occurring?  I am using Weldwood as the adhesive and stitching the inside box and outside perimeter.  The leather is 2/3 veg tan on both sides.  Lining leather too thick? 

2.  The thread is picking up alot of the dye.  I am dying the leather with oil based dye and sealing with a 50:50 Resolene waiting overnight before gluing and stitching. 

As always, your advice is greatly appreciated!
 

[Mattsbagger]

As to dye transfer I let dye dry for a day or two. Then punch my stitching holes. Then top coat.  Dry another day. And last is stitching. Then my edges. The wrinkling is always an issue unless on piece is slightly smaller do to stretch and compression. But then it won't lay flat if corners are not pulled up. Picture would help.