So the problem, as I see it, starts shortly after point (iii) above: what about strings that begin with 002? To find those cases, you must find strings of length $n-3$ that do not have 11 in them. This is some amount less than $a_{n-3}/2$, but how much I don't know. (the 112 case is similar)
So to solve this, I'd divide the problem into several classes, find a recurrence relation for each class, and then combine that to obtain a recurrence for the sum.
So then, let's define a few cases:
$a_n$ will be the original sequence, the number of trinary strings of length $n$ that do not contain both two consecutive 0s and two consecutive 1s
$b_n$ will be the number of trinary strings of length $n$ that do contain two consecutive 0s, but do not contain two consecutive 1s
$c_n$ will be the number of trinary strings of length $n$ that do contain two consecutive 1s, but do not contain two consecutive 0s
$d_n$ will be the number of trinary strings of length $n$ that do not contain either two consecutive 0s or two consecutive 1s
Note that $a_n = b_n + c_n + d_n$.
Now, for $i = 0, 1, 2$, let $a^i_n$ be those strings be those strings of the kind we're looking to count to make $a_n$ that begin with the digit $i$. So for example, we have:
$$a_n = a^0_n + a^1_n + a^2_n$$
Similarly, define $b^i_n$, $c^i_n$, and $d^i_n$.
Now, consider finding a recurrence relation for $b_n$; it's easiest to break that up into recurrence relations for $b^0_n$, $b^1_n$, and $b^2_n$.
Straight from the definitions we get:
\begin{align}
b^0_n &= b_{n-1} + d^0_{n-1} \\
b^1_n &= b^0_{n-1} + b^2_{n-1} \\
b^2_n &= b_{n-1}
\end{align}
Remember, we're looking for strings that do contain 00 but do not contain 11. For such a string to begin with 0, that means that the rest of the string either already met our condition ($b_{n-1}$ cases) or was a string with no consecutive 0s or consecutive 1s that started with 0 ($d^0_{n-1}$ cases). For such a string to begin with 1, that means that the rest of the string already met our condition and began with a 0 or a 2 ($b^0_{n-1} + b^2_{n-1}$ cases). For such a string to begin with 2, it means only that the rest of the string matched our condition. ($b_{n-1}$ cases)
To reduce the number of different series we're dealing with, let's try to eliminate the series $b^i_n$ and leave ourselves with only $b^i_n$ and $d^0_n$ on the right hand sides:
\begin{align}
b^0_n &= b_{n-1} + d^0_{n-1} \\
b^1_n &= b_{n-2} + d^0_{n-2} + b_{n-2} \\
b^2_n &= b_{n-1}
\end{align}
Therefore:
$$b_n = b^0_n + b^1_n + b^2_n = 2b_{n-1} + 2b_{n-2} + d^0_{n-1} + d^0_{n-2}$$
By similar logic, we can derive a formula for $c_n$:
$$c_n = 2c_{n-1} + 2c_{n-2} + d^1_{n-1} + d^1_{n-2}$$
Note that we already have a a recurrence relation for $d_n$ from the original problem:
$$d_n = 2d_{n-1} + d_{n-2}$$
Also note that $d^2_n = d_{n-1}$ and therefore
$$d^0_n + d^1_n = d_n - d^2_n = d_n - d_{n-1}$$
This will come in useful later.
Now then, for $a_n$:
\begin{align}
a_n &= b_n + c_n + d_n \\
&= 2b_{n-1} + 2b_{n-2} + d^0_{n-1} + d^0_{n-2} \\
& \qquad + 2c_{n-1} + 2c_{n-2} + d^1_{n-1} + d^1_{n-2} \\
& \qquad + 2d_{n-1} + d_{n-2} \\
&= 2a_{n-1} + a_{n-2} + (a_{n-2} - d_{n-2}) + d_{n-1} - d_{n-2} + d_{n-2} - d_{n-3} \\
&= 2a_{n-1} + 2a_{n-2} + d_{n-1} - d_{n-2} - d_{n-3} \\
&= 2a_{n-1} + 2a_{n-2} + (2d_{n-2} + d_{n-3}) - d_{n-2} - d_{n-3} \\
&= 2a_{n-1} + 2a_{n-2} + d_{n-2}
\end{align}
Almost there. We can now work to eliminate the $d_{n-2}$ terms, but first notice that this last equation can be rewritten as:
$$d_{n-2} = a_n - 2a_{n-1} - 2a_{n-2}$$
And therefore these two equations follow:
\begin{align}
d_{n-3} &= a_{n-1} - 2a_{n-2} - 2a_{n-3} \\
d_{n-4} &= a_{n-2} - 2a_{n-3} - 2a_{n-4}
\end{align}
Now, applying the recurrence relation for $d_n$ again:
\begin{align}
a_n &= 2a_{n-1} + 2a_{n-2} + d_{n-2} \\
&= 2a_{n-1} + 2a_{n-2} + 2d_{n-3} + d_{n-4} \\
&= 2a_{n-1} + 2a_{n-2} + 2a_{n-1} - 4a_{n-2} - 4a_{n-3} + a_{n-2} - 2a_{n-3} - 2a_{n-4} \\
&= 4a_{n-1} - a_{n-2} - 6a_{n-3} - 2a_{n-4}
\end{align}
So that's the final recurrence relation:
$$a_n = 4a_{n-1} - a_{n-2} - 6a_{n-3} - 2a_{n-4}$$
This is something of a mess, but it checks out:
\begin{align}
a_0 &= 1 \\
a_1 &= 3 \\
a_2 &= 9 \\
a_3 &= 27 \\
a_4 &= 79 \\
a_5 &= 229 \\
a_6 &= 657 \\
a_7 &= 1871 \\
a_8 &= 5295
\end{align}
Those values were calculated with the recurrence relation and verified by the python program:
import itertools
def find_a_sub_n(n):
c = 0
for q in itertools.product(*([['0','1','2']]*n)):
h = ''.join(q)
if not (('11' in h) and ('00' in h)):
c = c+1
return c