BCS and FPS connectors

[1gboost]

I recently sent my ecu out to ECMTuning and they discovered that I was right about a loose connector but I also had a blown capacitor. They told me the cause for this blown capacitor could be from a short in the BCS and FPS connectors. I go out to the car to check these connectors and both have been unplugged. I have an aftermarket FPR and intake. I don't know if I can even plug the BCS into anything but the female connection is still available for the fps connector. All of the unplugged connectors are very dirty. Should I reconnect my fps connector even though I have an aftermarket FPR? Also, I have a truBoost gauge which I honestly do not like at all. I've considered stripping it out and putting in a manual boost controller and a regular boost gauge but would this affect my BCS?
Any advice or knowledge on what I should do with these connectors would be greatly appreciated, thanks!

 

[TSI_93]

You can plug the BCS and FPS back into the wire harness. If they are hooked up via vacuum line they really won't do a whole lot of anything.

 

[1gboost]

I should have been more specific, I was referring to the electrical connectors. Also, the BCS does not have a female connector present to plug the male fitting into. I can go double check but I believe the female end is located on the stock aircan?

 

[TSI_93]

If memory serves me correct, it should be on the passenger side frame rail near the fuse box.

http://www.dsmtuners.com/forums/151542249-post31.html

 

[1gboost]

My question is, after reading what I could find about these two connectors, given that I have an aftermarket intake and FPR, will leaving these disconnected cause me to blow my capacitor again? In other words, for the people out there also running an after market FPR and intake have you ever had or know anyone that has an indirect failure to their ecu due to these unplugged electrical connectors? Furthermore, what impact does it have on my car to leave these unplugged?