Be patient
I'm afraid I don't see any very easy way to truly solve the issue, but I'll have a try. It would not be hard if you wanted to delay the subs, but to delay the mains is harder since it is more quality critical.
One way of doing it would be to use a very high quality ADC after the pre-amp, then use a digital delay (~5ms for 6'), then a nice DAC and then on to the power amps. The signal to the subs goes direct from the pre-amp.
Another way that is better, but requires a big system change is to take the signal from your transport, put it through the digital delay and then on to your DAC, pre amp, power amp and main speakers. Then you take another line from the transport (could be looped thru from the digital delay but without any delay added, something like the Behringer DEQ2496 can do the job) and pass that to another DAC without it being delayed and that goes to the pre-amp, another power amp and subs.
The problem here is that you need a pre-amp which can control the volume of 4 channels (2 for the subs and 2 for the mains). Such a pre-amp can be done, I have one which does 6 channels for my digital active system using 6 S&B TX-102 transformers and a custom built 24 position switch from Greyhill. Music First Audio might be able to make something similar.
It depends how attached you are to your preamp and if you even use a digital front end with a DAC.
Yet another option is to use an analogue active all pass filter (phase shift) before the power-amp of the subs. However, this is not the same as a true time delay on the mains. It can get the two signals to arrive in relative phase at the Xover point, but the subs will still actually be delayed by their physical offset.
Another similar option is to position the main speakers and subs so that they are exactly 180degrees or 360degreese or 540degrees etc... delayed at the Xover point. If you crossed at 100Hz then the main speakers could be 1.72m, 3.44m, 5.16m etc.. in front of the subs. With a sharp Xover (24dB/Oct or greater) that should not cause too significant an issue.
I would probably try the all pass filter on the subs as a first course of action. Depending on the amount of delay and at what frequency this may or may not be audible. A lower Xover is better in this case. I expect someone like Oedipus knows more on that subject.
Having said that, one of the advantages of a large IB sub is minimal group delay and that would go out the window with that 6' delay between the mains and the subs, whether or not it is supposed to be audible.
As for the EQ… well I am horrified that you would not use it
If you have a digital source (transport and DAC) then you can place the EQ between them in the digital domain and get practically nill negative effects. Also, it can do the digital delay at the same time if you were going for the option with the 4chanel pre-amp.
Or, you could place it in the line of just the subs, but that would introduce yet more delay (~1ms) so you would need to Xover even lower.
