Data format for gnuplot plot

gnuplot doesn't like data in rows. You could transpose your data with an external tool and simply plot it as columns with gnuplot. Unfortunately, gnuplot has no transpose function itself, although, in principle you could also transpose with gnuplot (https://stackoverflow.com/a/65576405/7295599), but it's probably highly inefficient for large datasets.

Actually, here is an awkward gnuplot solution to plot data from two rows. The values of the rows of interest are stored in arrays (hence requires gnuplot >=5.2.0) using a dummy table. The option every ::SkipCols skips the first SkipCols columns. In your case SkipCols=1 which skips the time values. Maybe somebody can simplify this approach further.

Code:

### plotting a row versus another row (requires gnuplot >=5.2.0)
reset session

$Data <<EOD
0.0   0.1  0.2  0.3  0.4  0.5  0.6  0.7
0.0   1.1  1.2  1.3  1.4  1.5  1.6  1.7
1.0   2.1  2.2  2.3  2.4  2.5  2.6  2.7
1.0   3.1  3.2  3.3  3.4  3.5  3.6  3.7
2.0   4.1  4.2  4.3  4.4  4.5  4.6  4.7
2.0   5.1  5.2  5.3  5.4  5.5  5.6  5.7
EOD

myXrow = 2      # counting starts from 0
myYrow = 3      #
SkipCols = 1    # skip number of columns from the beginning

stats $Data u 0 nooutput            # get the number of columns
array X[STATS_columns-SkipCols]     # define array size
array Y[STATS_columns-SkipCols]     #
myX(row) = ($2==row ? X[$1-SkipCols+1]=$3 : NaN)
myY(row) = ($2==row ? Y[$1-SkipCols+1]=$3 : NaN)

# put the x,y rows into arrays
set table $Dummy
    plot $Data matrix u (myX(myXrow),myY(myYrow)) every :myYrow-myXrow:SkipCols:myXrow::myXrow+myYrow w table
unset table
undef $Dummy

set key noautotitle
plot X u 2:(Y[$1]) w lp pt 7
### end of code

Result:

Addition: (Version for gnuplot 5.0)

Here is a version for gnuplot 5.0. Although datablocks have been introduced in gnuplot 5.0 you cannot address them via index as you can do in gnuplot 5.2. So, this workaround uses strings to store the rows and then printing it back into a datablock. Not very elegant and probably not efficient, but it seems to work. Unless there would be a limit of the string length, it should also work for your 500 columns. Actually, you have comma as separator, so you have set datafile separator comma and later set datafile separator whitespace. The code can probably still be optimized.

Code: (Result same as above)

### plotting a row versus another row (working for gnuplot 5.0)
reset session

$Data <<EOD
0.0,   0.1,  0.2,  0.3,  0.4,  0.5,  0.6,  0.7
0.0,   1.1,  1.2,  1.3,  1.4,  1.5,  1.6,  1.7
1.0,   2.1,  2.2,  2.3,  2.4,  2.5,  2.6,  2.7
1.0,   3.1,  3.2,  3.3,  3.4,  3.5,  3.6,  3.7
2.0,   4.1,  4.2,  4.3,  4.4,  4.5,  4.6,  4.7
2.0,   5.1,  5.2,  5.3,  5.4,  5.5,  5.6,  5.7
EOD

myXrow = 2                 # counting starts from 0
myYrow = 3

set datafile separator comma
X = Y = ''
AddValue(S,row) = S.($2==row ? sprintf(" %g",$3) : '')
set table $Dummy
    plot $Data matrix u (X=AddValue(X,myXrow),Y=AddValue(Y,myYrow)) every :myYrow-myXrow:1:myXrow::myXrow+myYrow
unset table
undef $Dummy

set print $DataNew
    do for [i=1:words(X)] { print sprintf("%s %s",word(X,i),word(Y,i)) }
set print

set datafile separator whitespace
set key noautotitle

plot $DataNew u 1:2 w lp pt 7
### end of code