Hmmmmm. I live in the waukesha area and see loads of cars coming out of LMT. I've spoken with a handful of happy customers as well. They do seem mostly GM based but have had numerous coyotes come out of their shop. I used them for a header install and have only positive things to say.I would avoid LMT at all costs. They are about 90% GM and 10% other. Word on the street is they blow cars up and then blame the owner of the car because it wasn't "built" by them.
I can't speak on Livernois Tuning but have heard good things from other.
I am tuned by Lund Racing (HP Tuners; they also tune with SCT). I have their nGauge and their FlexFuel tune.
Other good tuners that do remote tuning: AED (SCT), VMP (SCT), and Palm Beach Dyno (SCT).
As far as intakes go, I run a JLT with an oil filter. The stock intakes actually flow pretty well with a drop in filter.
Others have had great luck with a PMAS intake; very similar to the JLT.
You could even try going with a GT350 cold air intake with the throttle body and may have some nice pickups.