Preamp no longer makes a difference after caps and wire

I just wanted to check if anyone else had this experience. My tube preamp use to be pretty important at removing the harshness from my dac. Since I’ve upgraded the wired in my whole system and caps on my speaker they gave the system a tube like quality. I’ve been skipping the tube in the preamp and the difference in sound is almost minimal. I think I would have a hard time a/b the difference. 
What do you mean skipping the tube? Do you mean it's still there but doesn't make a difference sonically?
I can turn the preamp off, and it just bypasses it. 

Even when I turn it on the difference are extremely minor to warrant keeping it in the system generating heat. 
What is meant by 'I’ve upgraded the wired in my whole system'?
Did you replace all the wire in your power amplifier, DAC and speakers??
Or just the interconnect cables?
replaced all IC, and speaker cables. 
Still don’t quite do you “bypass” the preamp? Do you have some sort of switch ahead of your amplifier and you switch between the preamp and direct DAC connection and use the DAC volume control?
@thewatcher101 - Please list the pre-amp you are using.  
A lot of people claim that cables take some time to break in. I've been doing this long enough that I don't question these claims; if I were you I wouldn't sell anything until you've had some time on the system. It does not matter if the cables break in or not- it may be you that has to get used to the system sound; but whatever it is it might well be the case that although you can't hear what the preamp is doing now, you may well hear it after a few weeks of playing the system as it is now.
'I always tell people make one change at a time, and then take plenty of time to live with it so you know you did it right (or wrong as the case may be).
@thewatcher101 - The  Pathos Aurium is a headphone amp. I'm not familiar with it, but I looked it up. The only "outputs" it has are for headphones, plus an 1 XLR and 1 RCA "Tape" output. In this unit, I'm not sure what the difference might be for a "tape" output vs a traditional pre-amp output. I'm not sure you are using it as intended and I'm not sure any advice you may get will be valid considering it is not a traditional pre-amp.

Just curious, how do you have this connected to the amp that powers your speakers? What amp are you using?
I guess this brings up the old issue of active pre or passive pre...or no pre! Everyone has a different opinion of course, and many listeners seem to think that the more that you can eliminate form the signal path the better. I have tried nothing as well as passive twice, and for me, I will always use an active pre. Something is just lost without it...body and three dimensionality.
After bypassing the ignition system in the Morris Minor the engine became dead quiet. No grain, no jitter, no dither, no digital glare.
Update, after a few more session of listening with it on and off, the conclusion is still to keep it. When the volume is turned to listening levels. The tubes even though impact no significant sonic signature that I can pin point, but the higher sense of realism it imparts. Usually with gear, you can tell  what it is doing, but with this preamp and the tubes I am using, the changes are so subtle but significant. By trying to identify what it was doing, I kinda of lost the point to just feeling how my system was delivering music. Very interesting
@thewatcher101 - What Amp are you using to power your speakers?
Sounds to me like some has designed and manufactured the "worlds best preamp", the mythological "straight wire with gain"!!!!! No colourations/distortions just the sound of, well, like going direct with source to amp.

Cheers George
It took a lot of tube rolling to get here, I've tried some really nice 'holy grail' tubes from telefunken, siemens, mullard, and russians. 

Turns out they all had coloration, the only ones that were neutral to my ears were matsushita/national - some very inexpensive tubes. 

They are biamped - audiosource 310v for woofers and mini mite monos for hf. 

The preamp was recommended in one of the last few articles written by Arnie Nudell. 
What amp are you using? 
The Pathos Aurium is a headphone amp, not a pre-amp. I read the user manual. According to the user manual, the "tape" outputs are a bypass. To me that implies that the tube and headphone amp are not in the circuit at all if you use the outputs.

I suspect you may not be using the Pathos properly. That would explain why you don't hear any difference when you turn off the Pathos. 

How are you "skipping" the tube in the pre-amp"? Are you turning off the Pathos?
All this tells me is that your DAC is much better than the rest of your system, and your speakers must not be very good. I've heard good balanced systems from moderate to very expensive and the preamp always makes a large difference!
You might be right, the dac is Mirus Pro speakers are JBL 4319 recapped with mundorf supreme. The DAC by price is twice the speakers.

But the preamp now is significant if you don't try to look for what it is doing, because after some time, the music isn't very engaging without it. 
I would talk with Pathos and describe your goals for the unit and how it is hooked up, I think they are in a better position to tell you how to proceed