Do to lack of reasonable tools (I know I shouldn't blame them ) I was only able to route a binding channel half as deep as I need it. So I have 2 options.

1.) use hand tools to dig it deeper
2.)put the binding in as is and cut off alot of the thickness to make it flush.

Any ideas on which I should do, and how are much appreciated.

In the nicest way possible, (honestly dont mean this to sound mean =p)
Dont half ass the job, the guitar can wait, rather than have it screw up cause your in a hurry,
is their any way you can route it again to double up the hole?
I Love Oreos, And im English =D
So how do you recommend I cut the groove deeper? What I did the first time was jerry rig a template follower bit with a smaller bearing than it should've had, and the surface of my guitar was still flat (it's now carved). I mostly only have hand tools, and there are some odd contours I'll need to get into. What do you recommend?

And about the time thing, I agree fully, it's just that I have an unchangeable deadline.
There's not much more frustrating than trying to do a job with the wrong tools, is there?

Good luck to you man. I hope you can get the right tools for the job before you get too much further into it.
"People never misapply their economy so much as when they make mean provision for the education of children. The only practicable method to reform mankind is to begin with children." -- Noah Webster