ghostgimli

Сам задался вопросом пока искал, подредактировал ваш код и получился рабочий
P.s. Поздновато, но может для будущих поколений будет в тему

text = input('Введите текст : ')
text = [x for x in text]
res = ''
m = [
    ["Н","И","К","О","Л","А"],
    ["Б","В","Г","Д","Е","Ё"],
    ["Ж","З","Й","М","П","Р"],
    ["С","Т","У","Ф","Х","Ц"],
    ["Ч","Ш","Щ","Ь","Ы","Ъ"],
    ["Э","Ю","Я",".","-","_"],
    ]
for i in range(1,len(text)):
    if text[i] == text[i-1]:
        text.insert(i,'Я')
if len(text)%2 != 0:
    text.append('Я')
print(text)
for k in range(0,len(text),2):# Берём по два аргумента
    x1=-1;x2=-1;y1=-1;y2=-1
    for i in range(6):
       for j in range(6):
           if x1 == -1:
              if text[k] == m[i][j]:
                  x1=i;    y1=j
           if x2 == -1:
               if text[k+1] == m[i][j]:
                   x2=i;    y2=j
    if x1== x2:
        if y1==5:
            y1=0
            y2+=1
        elif y2 == 5:
            y1+=1
            y2=0
        else:
            y1+=1
            y2+=1
    elif y1 == y2:
        if  x1 ==5 and x2 ==5:
            x1 = 0;     x2= 0
        elif x1 == 5:
            x1=0;   x2+=1
        elif x2 == 5:
            x2=0;   x1+=1
        else:
            x2+=1;  x1+=1
    else:
        temp=0
        temp=y1
        y1=y2
        y2=temp
    text[k]=m[x1][y1]
    text[k+1]=m[x2][y2]
print(text)