2005 chevy trailblazer 4.2 engine. Was driving on interstate engine intermittently began to run rough similar to a miss. Then check engine light was blinking for a minute or two then went off and engine ran smooth. Problem reoccurred several times, then once off the interstate pulled up to a red light and engine at idle was very rough, changining between 500-650 rpms. Parked the vehicle for several hours then drove it again, ran smooth till engine warmed up then the rough idle began. The check engine light is off now.

First you need to have EBCM - electronic brake control module check for DTC'S - diagnostic trouble code's . If the light is on there is a code stored . I think most part stores can do this and for free . After you find out what code is stored , looking up that code in service repair information for diagnostic trouble shooting chart would be next step . There are a few codes too.
DTC C0035 or C0040
DTC C0045 or C0050
DTC C0110
DTC C0131
DTC C0161
DTC C0186
DTC C0196
DTC C0201
DTC C0240
DTC C0241 or P0856
DTC C0244 or P1689
DTC C0245
DTC C0283
DTC C0287
DTC C0290 or C0292
DTC C0455
DTC C0550
DTC C0558

Find the code do the diagnostic's , fix the problem , wiring issue's , a sensor , bad module ,what ever it is . The light will go out then . Here is a sample of code discription .
• DTC C0035 Left Front Wheel Speed Sensor Circuit
• DTC C0040 Right Front Wheel Speed Sensor Circuit

Engine misfire ! Flashing check engine light , catayltic converter damaging misfire . Been on for three years ? No inspection were you live ? Flashing check engine light CarMD

Here's a video showing you where the fuse is. Check Engine Light Code P0410 Secondary Air Injection System Chevy Blazer...

run the fault codes
check for problem torque converter servo/ solenoid , VSS or TCM units

check fuel pressure regulator for fuel in vacuum line ,check fuel filter , and alot of those models needed a top engine clean where u drip top engine cleaner through the air tube to clean valves .
we have done this action quite a few times with good results where i work
for some reason these 4.2 ltr engines seam to gum up on valves alot

your timing belt on your vehicle is connect and turns the a/c pump if it run rough with the air on you may either have a vacuum leak in a hose or either your ac pump may be going out

I work for a chevy dealer I will look into the problem and get back to you.

cylinder 5 has a dirty or sticking injector. check pvc and egr valve.

map sensor. check your spark plugs, wires, etc. maybe a loose wire plug. did u mention check engine light, i wonder can you tell me what diagnostic code came up. go to ur nearest auto parts if u dont have a scanner. and pull them codes out.

Could be either a failing gauge or a failing sending unit on the fuel pump. Check out this blog post about a similar problem in Trailblazers - http://drspeedometer.com/chevy-trailblazer-fuel-gauge-quit-working-top-2-reasons-why