The blower is working fine and the furnace ignites all right, but the furnace can take over an hour to raise the temperature to the mid sixties and sometimes trips the high heat sensor.

Is filter clean? Are all the vents clear and open? Is there anything covering or blocking the fresh air returns? Are all the supply ducts intact and blowing air? What is the temperature of the hot air coming out vents? Do you own and able to use a amprobe meter to see that the blower is pulling the right amps ? Does the blower seem to be running consistent speed?

I've checked all ducts and the fresh air returns and they are free and clear. The blower is blowing a lot of air, but it isn't real warm. The furnace has run for over an hour and the temperature in the house doesn't get more than 65.

Are all the burners working? If not might need cleaned. The flame while burning are they all nice and blue with little yellow tips and somewhat even,,

How would I go about that, the flame coming from two of them have quite a bit a yellow in them.

but the furnace can take over an hour to raise the temperature to the mid sixties and sometimes trips the high heat sensor.

the flame coming from two of them have quite a bit a yellow in them.

Something is very wrong with this picture from what you have posted so far. I believe for your safety sake you will be better served by having your furnace checked and serviced by a on site professional HVAC company. You might have a gas pressure problem along with a overheat condition that has caused the high heat limit/sensor to trip. Better to be safe than sorry.

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Not a job for the novice, yo9u will need to kill the power,cut off the gas,take loose the gas valve and the wiring,to gas valve ,the manifold can come loose with the gas valve attached, clean the orfaces with a very strong wire be sure not to let anything break off in the tiny holes that the gas come out of, if you think of blowing it clean with compressed air,don`t blow backwards toward the gas valve you don`t want to blow dirt back into the gas valve,, replace exactly as you removed
If you don`t feel comfy, it might be better to have a tech to do this

If the high limit trips, have the A/C coil checked for dirt blockage.

Yes we do and lots of it

I had the same problem. The furnace was on all the time (It's cold outside) but the house wasn't heating over the mid 60's. Not only that but there was something (not gas) that was burning my eye's and nose when I came in to the house from outside. I checked everything and even bought a new O2 monitor thinking my other one was bad. No CO. I finally looked in the furnace to see that the burner flames weren't going into the heat exchanger, or at least not the way they are supposed to. I shut off the furnace and started to investigate. I had to pull off the power vent, the plastic cover behind it and the metal heat exchanger cap above that.
My eye started to burn real bad. Ah, the source of the problem! (I'm so happy I found out what it was, not knowing is terrible)
Turns out the coating that is used to prevent rusting had broken free and was clogging the heat exchanger. This in turn created more condensation which turned to mold and mildew within the furnace which was burning everyone's eyes and nose.
I cleaned most of the broken coating from the exchanger but some are still restricted. 80% better then it was.
Got it back together, fired up the furnace and teeda, I have heat! And the heater shut off for a long period which it hasn't done much in about a week. I'm going to hate this next bill.
Anyway, I couldn't remove all the material so I'm looking for a heat exchanger today!. Something to look into.. Good luck.