If I was going to do a awesome trail machine I would do the 4 mill. It helps ad midrange torqe due to the extra stroke. I would do a hot trail port and ethire keep the stock carbs or go with dual PWK 28's. A 2:1 kills the top end.
For exhaust I would talk to the guy doing the port job. He will know what works best with his port jobs. T5's would be a mid to top end pipe, CPI's are a top end pipe, and Paul Turner Mids are a great low end pipe.
I woudlnt let your local guy do the port job by the what you said he says.