I think
@bdstone914 may have had a great solution.
Blocked off the tunnel with clay. I believe he doused it liberally with Evaporust. Probably via garden sprayer or similar. Let sit, rinse, repeat?
Others have done similar with Ospho
You could cut some tuna can flaps here and there to aid access to the multiple holes already there. What you don't want to mess up is the relative positioning of the shifter relative to the rest of the tunnel.
However, given how deep you are already in, and assuming that you have floor pan sections, why not just open it up from the bottom and replace the floorpans underneath it? This is the more robust way to get good access to the tunnel and to fully assess the control tubes.
Not sure how far gone your tunnel is, but, in my case, I just removed the whole thing it was so bad. Replaced with donor from another car. Many cars have donated so this car can live.
Pictures of what you're dealing with are helpful to community both to help you and to learn from. What works and what doesn't.