Hi Bomp,
I'm sorry to hear about your problems, it all sounds very frustrating
I hope you don't mind me saying, but you have quite a large layout with a few circuits, you have points, etc, and now you have signals.
I would suggest attacking the problem in stages, firstly, uncouple everything (and I mean everything)!!
Then go around your whole layout and look if there are any metal objects or anything conductive across the rails.
Then check that if you've got electrofrog points, there is an insulated fishplate on the frog part of the point to each rail (That's the two inside rails at the heel of the point)
Then if it is all clear, and insulated fishplates are in place, wire one circuit/section up at a time. if there are any points within each section, throw each and every point in that section, and see if anything shorts out.
Doing this one section at a time should enable you to narrow it all down, and may help with the frustration. I have had a few frustrating moments with my layout, from incorrectly connecting feeds to one of my Cobalts, to forgetting to slice the wired link on an electrofrog point. But I've always found a nice brew, 5 mins chill , and starting from scratch, the easiest way of fault finding.
As far as the colour light signals go, I would most certainly leave them till the layout is working as you want it first, as this can just compound any problems you have!!!
I wish you all the best and I hope the problem comes to light sooner rather than later.
Regards
Jinty ;-)
Edited to say, You're already working from the beginning, I should of read more!!!!!!!
Also, there shouldn't be any problem with having feeds at the toe of a point, it's any feeds at the heel that will cause problems ;-)