Also with setting up your cold start maps, decrease the fuel for the current cold temp range, eg 18C>25C till the engine begins to idle up because its lean and then increase the fuel again till the car bogs down past it was normally. Exactly half-way between these two points eg between 0.9ms and 1.4ms is the best value for that particular cold map. Go through and do them all.
As for the idle up, if you have a single stage idle up solenoid or something similar you can wire it off the Microtech. Wire it off normally closed contact of a relay and wire it to the thermofan output. Set the the switch on temp of the thermo fan to say 65C and the idle up will turn on whenever the engine is below 65C.
Are you controlling the timing through the microtech, its the best method. If your just using the dizzy and vacuum advance you may not be getting the correct value of advance and thats why you are experiencing some flat spots and rough running.
Who has done the tuning, i'd get someone who knows what they are doing with it otherwise it will cost you alot of time and money. A reputable place with experience will pretty much know off the top of their head rough values for certain parameters like the pumps and how much to add.
Also, trust the wideband sensor they use on the dyno not your one you've hooked up to the Microtech. They are much better, reliable and accurate. The factory o2 sensors are only really good for values around 14.7, as you get further away from 14.7 the specs of the sensor show its signal becomes dodgy.