I don't see the problem from your photos (nice build by the way).
I prefer using gel stains when I stain. I sand to 220. Seal the wood with a 'spit' coat of blond shellac. Light sanding to smooth the surface again. I wipe the stain on with a small clean rag and immediately wipe off all excess with a clean rag. Not dark enough? I give it another coat the same way. If it's really not getting enough color I may let it sit for 10 minutes, but as mentioned in an earlier post, they don't absorb. I nearly always practise on a cut-off piece of the stock I'm working to ensure the color and intesity is what I'm after.
May the grain be ever in your favor.