Good news, I now have the program and data on 2 separate 64 K cards , the first one is the data disk with com files on it, you run it first, only once, then you take the card out and if necessary reformat it and put disk 2 the program disk on it, but it is easier to  use two separate cards. This way you install all of the data files on drive C first, then take out the fist card and put in the second card with the program and pbrun.run file on it, once it is in you cannot swap disks while it is running , as it uses .run files.

Theoretically you could run this program with only one 64 K card, by doing what I have said in the above, as once you have installed the data on drive C you no longer need the install card. 

I have 2 separate batch files for creating 2 different cards if you have  card reader and a compatible computer, if not then create card one (the data card) use a parallel port or serial port  to transfer the files to the first card, run the setup program, it will take several minutes to install the data to drive C, (after fdisking it to 45 K by typing fdisk 45, follow the instructions)  and then run setup.

Since you do have a backup of all of the files in my zip file , you can format that card and put on the program disk.

Making the program disk without a Card Reader:

Skip all of the below stuff and run the batch file called : 'buildft' if you have a parallel interface.

First format your 64K card with your Atari Portfolio, then use a serial or parallel port to transfer the following files in the following order to your program card (in the portfolio).

PBRUN.RUN
PLOTTMAX.RUN
RUNME.BAT

There you go, you now have a working card for the program disk, write protect your disk, as you will not be writing to it at all, all data files are read/write from drIve C only.

Making the data disk without a card reader.

Format your 64 K card first in your Atari Portfolio,  then use a serial or parallel port module to transfer the following files in the following order to the data card (in the Portfolio).

PBRUN.COM
SETUP.COM
RUNFIRST.BAT

There you have it, two separate cards, (or in the case of only having one card, use the second setup first, the use the first setup last).

Running the Program for newbies:

First prepare your drive C to have enough room on it for the data files, if you have at least 30 k skip this step.

To do this type 'fdisk 45' at any prompt (a: or c:)

Follow the instructions.

I don't have to tell you to put in the data disk in the card slot, but I might have to. Run the setup.com program by typing the folloing on your AtariPortfolio.

'a:'
'runfirst'

Follow the instructions.

This one will take 3 mins to run, and display dots on the screen for each line of data loaded onto drive C of the Atari Portfolio.

When done the program will print 'Program Finished' on the screen.

close your Portfolio.

Take out the data card, then put in your program card.
At the same prompt, (a:) type 'runme'

It will take a while to run the program, maybe 3 mins.
Follow the visual Instructions.
Note that while running this program card, you MUST NOT remove the program card until you have exited the program by pressing the escape key. Doing so will corrupt your program card, especially if it is running something when you remove the program card.

Enjoy.
Russ Campbell