If this is your first turbo, you may not be accustomed to the lack of power when the turbo is "off boost." Nothing is going to fix that. A 140 cubic inch engine without boost is going to be anemic. Even though our little turbo spools up quickly and at lower rpm than larger ones, it is a turbo.
There is simply very little power below 2,800-3000 rpm. You are not producing enough exhaust volume and velocity to spin the turbo enough to produce high boost, and, frankly, it is probably not safe for the engine to build high boost at rpm that low. Some have even suggested that a steady diet of wide open or agressive throttle below 3,000 rpm has been linked to bent connecting rods and engine failure. I'm not sure that is true, but dropping down a gear lets the turbo spool and eliminates any of those issues, which do seem to be common to this engine for all of us.
Trying to accelerate sharply below that rpm range is going to be disappointing, may cause some bucking or jerkiness, and will not be productive. It will also contribute to fouling your plugs. If you want to accelerate, as in pulling out to pass, on a turbo car and your rpm is below 3,000 rpm, you need to drop down one gear before getting aggressive with the throttle. That just comes with the car -- all turbo cars, IMHO.
And yes, if you don't have a flex joint or good isolated rubber exhaust hangers, that could account for the vibratin.