Porting and Pipe Question

I have a 2000 CR250 that I recently had Eric bore to 265 with mo-better everywhere porting. I called the other day to inquire as to what pipe would work best for this application and he recommended the FMF Gnarly. He said it works better because it holds heat in the exhaust better. This makes sense to me but I was wondering if, or how much top end I would lose? Additionally, I am wondering if it would benifit me to chage the pipe at all? (It currently has the SST on it)
I was reading Eric's book and he mentions that retarding the timing a bit helps with top end but is a little flatter on bottom. I was thinking retarding the timing with the gnarly pipe might be a good comination for overall improvement.....is that a dumb idea?

Just so you know:
I would consider myself an intermediate rider and I primarily ride motocross and to a lesser degree offroad trails ect.

Also, I was looking at my cylinder when I got it back from Eric. Other than epoxy in a couple of locations and some apparent work on the exhaust valve, I could find no evidence of the porting. Is this correct for the Mo-better everywhere porting? It makes me wonder if we had some kind of communication mix up and he ended up just boring it.
He overbored my CR80 with the same porting, but the porting he did was evident on that one.

I realize my ignorance on this matter so I figured I would ask.

Thanks, I appreciate the information. It's nice to know that there is always a good place to have my lame questions answered by those who are in the know!