My best guess (and this is just an "educated" guess) is that the limit switches should be wired in series, with the thermostat.
You have 6 wires? How many cables? Usually there is a 2 or 3 wire cable coming from the thermostat, and there would be two wires from the 24V transformer, and 2 more wires to the gas control valve.
That would add up to 6 if you have only 2 from the T-stat.
First thing is to ID the wires from the 24V supply. That's easy, just power on the system, and use a voltmeter (set to AC volts) to check for 24V (give or take a few volts) on a pair of wires.
Wire from 24V (either wire) to 1st terminal of 1st limit sw (doesn't matter which one)
Wire from other terminal of same limit sw to terminal of other limit sw
Wire from 2nd terminal of 2nd limit sw to one wire to thermostat (doesn't matter which one)
Wire other thermostat wire to one wire from gas valve.
Wire other wire from gas valve to remaining wire from 24V supply.
Polarity is not important, since this is an AC system.
This is what I think it should look like.
You probably would have been better off (received more replies) if you had posted this in the Electrical forum.
Try this config, if it doesn't work, then re-post in electrical.