If we replace the most frequent character (1) with e we get:
98 7e28 +e38 4e55e6#$ +9e66+ e7#6 &$! @&$ *e +ee$ =o2 9#6e+
!o +ee # ?&7e 56&@e! o$68 o$e T
#$ 98 @o!e

If that is the case then the *e could be we, me, he, be...
+ee could be bee or see...
+ee$ could be bees or been or seen

you're on the right track...

see/seen seems more likely.
replacing + with s gives us:
98 7e28 se38 4e55e6#$ s9e66s e7#6 &$! @&$ *e see$ =o2 9#6es
!o see # ?&7e 56&@e! o$68 o$e T
#$ 98 @o!e

see$ could be seen or seed or perhaps seer
the preceeding *e gives us a better idea maybe.
me, he, be, we
"be seen" is the only thing that makes sense.
replacing * and $ with b and n gives us:
98 7e28 se38 4e55e6#n s9e66s e7#6 &n! @&n be seen =o2 9#6es
!o see # ?&7e 56&@e! on68 one T
#n 98 @o!e

the @&n before be seen has to be can
replaceing the @ and&with c and a
98 7e28 se38 4e55e6#n s9e66s e7#6 an! can be seen =o2 9#6es
!o see # ?a7e 56ace! on68 one T
#n 98 co!e

an! has to be and
replacing ! with d
98 7e28 se38 4e55e6#n s9e66s e7#6 and can be seen =o2 9#6es
do see # ?a7e 56aced on68 one T
#n 98 code

apparently the o wasn't encrypted?
so #n can't be on or an. replacing the # with an i
98 7e28 se38 4e55e6in s9e66s e7i6 and can be seen =o2 9i6es
do see i ?a7e 56aced on68 one T
in 98 code

Dang it! I haven't been on since early this morning. I missed code fun.

We still have 2 sets of doubles.
the 5's in 4e55e6in or surrounded by E's. They should be consonants, but which ones. I'll attack the 6's first. of the common doubles LL fits best there. leaving:

98 7e28 se38 4e55elin s9ells e7il and can be seen =o2 9iles
do see i ?a7e 5laced onl8 one T
in 98 code

We have a double appearance of 98 in the message. The last one seems to be "MY" replacing 9 and 8 with M and Y we get:

my 7e2y se3y 4e55elin smells e7il and can be seen =o2 miles
do see i ?a7e 5laced only one T
in my code

my 7e2y se3y 4e55elin smells e7il and can be seen =o2 miles
do see i ?a7e 5laced only one T
in my code

5 looks like it could be P. that would make
my 7e2y se3y 4eppelin smells e7il and can be seen =o2 miles
do see i ?a7e placed only one T
in my code

=o2 appears to be for replacing - and 2 with F and r we get:
my 7ery se3y 4eppelin smells e7il and can be seen for miles
do see i ?a7e placed only one T
in my code

7 is obviously V
4 is z
? is h
3 is x

my very sexy zeppelin smells evil and can be seen for miles
do see i have placed only one T
in my code

The T is not encrypted. my guess is that the comment is to point out that Nathan avoided the most common consonant in the english language.

very good!