Uneven Finish With Armstrong-Clark on Ipe Deck

I live in Virginia and am a new subscriber. I have a seven year old ipe deck. It was originally finished with Sikkens and  a maintenance coat applied every year. Looked fabulous for the first couple of years. Then started getting splotchy, dark and peeling in places. 

Recently had it sanded down and stained with Armstrong-Clark Mahogany stain.  The problem is the finish is very uneven. (See attached photo.)

I should have done more research before beginning this project. I realize now that two mistakes were made.

1. No deck brightener or other treatment was applied after the sanding; they just vacuumed off the dust.

2. They applied the single coat of stain with rags rather than brushes or stain pads.

I don't know if either of these helped create the uneven finish. But, the real question is, what do I do now?

Should we apply a second coat? If so, what prep should be done before applying it?

I would greatly appreciate any other suggestions. Please help!

Thanks