First off, I'm a long time lurker and long time tuner of other cars. Love this forum and seeing the innovation.

I'm running an m-box on a stage 3 2.7t setup making great power, no codes, overall great running engine. The tune is from a local, but nationally recognized tuner but am having difficulty getting them to finesse the code to my liking beyond simply max power.
Since leaving the stock programming behind and running this tune I've had low RPM and low load issues that are minor but annoying:

1. Off-idle (when letting out the clutch to get the car going) feels as though there is a lag or a non-linear change in fueling. It gets the car going after a half-second delay then a surge of power.
2. Shifting from gear to gear (when load changes from clutch in to clutch out) is a pain and inconsistent when getting back on the gas. Feels like it lugs much too easily as if my motor mounts are shot (they aren't). Mapping issue?
3. If I'm cruising in first at idle (only done in slow traffic) I get surging.
4. Blipping the throttle lightly and quickly from idle causes a slight drop in RPM. Blipping a bit more finally revs the engine. This is unlike stock programming which revs regardless of how light or quick the throttle blip is.

All this is minor but possibly related to some sort of enrichment/fuel mapping that's out of whack. The first few make driving the car a chore. Its not the smooth progressive programming I expect out of a dyno tuned setup from a known tuner. The power at WOT is great (400whp) and overall mid-throttle is good, but the low load transitions are driving me nuts and affecting clutch life during normal shifting.

Do you guys here have any suggestions as far as what maps or values might be off? Any specifics I should have them check?
I want to have some good insight into the issue before my complaints to the tuner are met with "don't drive the car at low RPMs," "not much we can do about that" and so on as I have gotten in the past. Although I've read through a lot of the Motronics info on this site I have no idea where to start.

I'd be willing to edit the file myself but since I'm still supported I'm hoping I can get them to work out the quirks. I'd appreciate any input you guys have. I've tuned all my other cars but bit the bullet with this one with my lack of free time recently. 

Agreed 100% with prj, as usual.

I do have to remind myself to think in terms of torque, prj. Its still habit to think in terms of simple old school VE maps.

I'm running the 52lb EV14s, stock 4 bar regulator, 85mm MAF. So, very typical set up.

One additional thing I noticed this morning is that most of the symptoms I described are worse on cold start, especially the throttle blip where the hesitation/rpm drop is much more pronounced. Does this still correlate with injector latencies?

Not to thread jack, but what about oscillation at idle without bliping the throttle, either in gear or neutral, latency as well?