I have a 2001 honda civic lx recently replaced tranny, alternator and battery was running great then starts acting up. I start it drive like 2 miles then the ac kicks off and cluster flashes battery light blinks then it looses power. Wait about 15 min then starts up and I loose power once warmed up any idea what it might be?

Remove and fully charge the battery; clean the battery terminals and cable connections; examine battery cables for corrosion and hidden breaks; and have the alternator tested. Most auto parts stores will test/charge batteries and test alternators for free. Static battery voltage should be around 12.75v and regulated battery voltage (engine running) should be 14 to 15 volts.

I suspect your alternator is failing, possibly due to worn brushes or a bad voltage regulator. On Honda alternators, the brushes and voltage regulator are difficult to get to. Re-manufacturers are not going to go to the trouble to break down the alternator as far as necessary to solder on new brushes and remove the voltage regulator. It's not easy removing the rear bearing, which must be done before you get to the brushes and regulator. Instead, the re-manufacturer will make a quick check of the alternator's electrical system, get it all clean and shiny, and put it in a box with some sort of warranty.

Car idling rough drive about 3 or 4 blocks the battery light starts blinking then my ac shuts off and loose power to vehicle.. Wait about 15 min and starts back up and does same thing again later is it the ICM or ignition switch

Your car doesn't have an ICM. Check for any codes or pending codes (Mode 7) with a scan tool. I guess you don't suspect the alternator? To me, you are experiencing classic alternator failure. Easy to have battery and alternator tested.