BE EXTREMELY CAREFUL removing the CNG tanks themselves.
First off, you should be able to verify that all your 3 separate safety valve (1 per tank) are functioning properly - AT LEAST that they will shut. Some valves can stick open or stick closed or work properly. If you can run a dedicated factory Ford CNG van about 200 miles you likely have all three tanks working where the valves are not stuck shut. You want to make sure they can (stay) closed - very important. A trained CNG mechanic was killed not checking this.
SO before you start this all,verify all 3 valves can be closed. Pull the electrical connectors to each valve. The design on 1998 AND BEYOND Ford valves is that they default to closed / shut when 12VDC is not run to the electrical connectors to the valves. The keyed ignition sends electrical current to the valves and opens them. No current to them, they should be all shut and not allow fuel out. So disconnect those connections at the valves.
With fuel still in the tanks, start the engine. The engine should run out of fuel in a few minutes. This should mean all of your valves can be closed. Again, very important to verify this. You do NOT want to mess with a valve that will not close and is malfunctioning and stuck open. It could be lethal.

Then, re-connect those electrical connections to the tank to allow the 3 valves to open again when you turn the key to ignition. Re-start the engine which could take a little bit to re-pressurize with fuel again.
Now, The very best thing you should do first is run that van out of fuel until it stops.
That will get you down under 110 - 120 psi which is what it needs to run the engine.
Then you would drain it at the coalescent filter area. That would empty the CNG fuel out downstream of the coalescent filter to the engine. However, the lines from the tanks and the tanks are still going to be full of CNG at around 110 psi.

My plan was to do this, then shut the valves off and disconnect everything. Then take the tanks somewhere to have them professionally drained and purged. If at low pressure I think I got a phone estimate of about $250 for the 3 tanks.
That can be done yourself but there's a lot of safety gear involved. Like a 15 foot deep metal ground or metal water pipe as a static ground (earth), a 10' + long discharge tube in the air with a high pressure valve etc... to do it by the book safely. The problem is when CNG is a very high or very low pressure and mixes with Oxygen it's extremely flammable / combustible then. Explosive. At high pressure of CNG O2 can't really get inside the tanks to mix so it's mostly a non issue. A leak ignited would simply turn into the worlds biggest flamethrower but not explode (this is what they say, and I saw a video of a CNG bus on fire that became a dual raging flamethrower as tank #1 and tank #2 melted their safety valves and vented to atmosphere and ignited in the bus fire - this occurred by design the way it was supposed to).
Here's a link to one like that:
The safety valves have a metal in there that's designed to melt and become an open hole when it hits a certain temperature - before the tanks get super hot and then explode.

But low pressure tanks where O2 can get into them can be explosive. The purge of CNG is tubed far away from the tank with that valve and after it's totally drained water or something like it (nitrogen) is pumped in there to completely flush out the CNG to atmosphere vent so there isn't the Oxygen with CNG mixture explosive potential.

 

FYI- once the tank is removed, you have to be licensed and the vehicle placarded to transport the tanks empty or loaded...the only time you can transport a tank like this is before it has ever had product in it. The shops that do this work, legally (fed) cannot allow the (non-permitted) delivery truck on the property since they have to have EPA license to receive such shipments and the documentation, etc.

IMHO, have the truck towed both ways.