If you're in the salt belt, there is probably some truth to the frame
rot. As for brakes and front suspension, remember that they have to
recommend replacement of everything that's even suspect for liability
reasons. If they didn't and say your tie rod failed on the way home they
would be liable. Not that I'm really trying to defend them as I think
most dealers have only their best interests at heart and are borderline
sleezy. The manifold studs is another common problem. By all means get a
second opinion but I'd have the frame checked before I put any real
money into it.

Keith,
your story is uncannily similar to what happened to me a year or two ago.
Brought my 94 PF (125,000 MILES - I think in KM yours is pretty close) in
for routine stuff - they said $1500 worth of brake work needed (calipers,
drums, etc) and some other stuff. The breaks had started sticking a few
days prior and there were other problems so I think they were legit.  They
also noted frame rot and said I might not pass inspection and suggested it
might be time to trade. I didn't want to hear that. I thought they were
just trying to set me up to trade. I had them do the repairs. Over the
next few months I poured a ton more $$ into the truck (starter, front
pipe, done by local mechanic). Had a local welding shop do the best they
could with the frame. So - I'm good for another 100,000 miles right?
WRONG. I wish I had listened to the dealer and traded right then and
there. Less that a year later, the frame rot caught up with me. Basically
the vertical bar that attaches the rear sway bar ripped right off the
frame due to rot. It became apparent that more welding would be needed if
I were to keep it, but I didn't even look into it. At that point I pulled
the plug and traded it in for a 2003 Xterra (before the thing literally
broke in two).
Love the X - it's almost the same truck, actually.
My mistake was being too attached to the PF and trying to keep it a little
too long, and I spent a lot of $$ trying to keep my baby alive. Get that
rot checked out by a mechanic, body shop, and/or weld shop. They should be
able to take a quick look for free. Check the frame around the rear wheel
wells. Tap on it - does it feel like you're going to poke through? Climb
under and take a good look your self.
I did a ton of research on this - some PF's rot out, some don't, and there
doesn't seem to be a correlation to salted roads or other environmental
things. If you got frame rot (not just surface rust) - run away screaming
before you put $$ into the other stuff. I still got pics of my frame rot
posted somewhere if you're interested or want more info - just let me
know.

Good luck and let us know how it goes.

John