I've replaced my furnace with a the echelon 8v during A/C season. The existing chronotherm T8600C1014 is about 20 yrs old. All was well during cooling season.

In heating the blower off delay is not responding as programmed on the board. It is set for 90 sec. When stat drops the call for heat the blower immediately starts its 15 sec slowdown to off. I recognized this problem early in the heat season when cycle time had 15+ minutes of off time. Once it got colder and off time dropped to less than 8 min I began to realized that a call for heat brought the blower on immediately; no 30 delay for the chamber to warm up. Gas valve would oopen about 1 min later. It turns out that when that happens it is because of an open limit (4 red flashes). After about 1 min of cool down it goes to slow amber flash and opens the gas valve for a normal cycle. - Except that it will not get a blower delay as programmed at the end of the cycle which will cause the whole problem to start over again. I have taken the chronotherm down and jumped R & W to confirm a normal cycle startup and correct blower off delay. Any suggestions of how the chronotherm may be confusing the timing circuit? Have never seen 24V phasing/ twinning error codes on the furnace.

What limit is it saying is open? Code should be on the door of the furnace. If it's a main limit check your return air filters.

Was the old furnace electric? Some thermostats can be set from gas to electric, if set to electric, the thermostat contols fan on, if set to gas, furnace contols fan on and off times. If old furnace was gas, and you have confirmed that furnace worked properly with stat bypassed, I would suggest just getting a new stat.

The code indicates "a primary or auxiliary limit switch has opened" (great help there!) Its not shutting down on limit open. It sees the open when it tries to start its next cycle if that new cycle is called for before the chamber cools on its own.

The thermostat does not have a gas/electric option (old furnace was Ruud gas).

I now have it just the R and W connected to the control board. As mygirlsdad indicated, I too believe it to be a thermostat issue. This is now more of a point of knowledge. Given just R&W connected, what could the stat do to that circuit to disrupted the dob when according to the install manual the fan off timer has 4 settings (60,90,120,180 seconds - factory set to 120) Zero isn't an option. Yet when I hear the thermostat click it shuts down gas and blower immediately.

Only thing I can think of would be if your stat has a heat cycle adjustment, or heat anticipator adjustment that needs to be set to requirements of new furnace. Other than that, just a fualty stat.