I didn't bypass my VATS, it's all in tact and operational - and mine starts just fine with no ECM (my whole ECM box is GONE!). I'm lost as to how you cut power to the ECM - if you pulled a fuse to do this, maybe that same fuse runs an ignition process. I don't know how to "test" for the swap working beforehand, I just did it, and made it work afterwards.
VATS will function without the ECM - no need to disable it really. But if you so desire, the tech article is here:
http://www.thirdgen.org/vats_passkey_system &
http://www.thirdgen.org/vats
And no need to hack up the wiring until you finish the swap and make sure everything functions - like I said it's been a blessing to have those wires from inside the cabin to outside the car - saves me from having to poke a hole in the firewall everytime I need a wire from inside to out - I just find an ECM wire that's not being used.
There are only 3 relays under the hood, one for the electric fans, one for the fuel pump (that won't be needed any longer), and one on pass side for the A/C system. So the only one that you can remove is the fuel pump relay, unless you run a seperate fan controller and remove the stock fan wiring (like I did).
I guess it all boils down to a JUST DO IT thing - if it's what you want. We'll help you get the bugs sorted out as you go. BUT - please know up front, it never happens in a weekend! I hate seeing folks that say "I have to have it done by Monday" - it's impossible. There's too many parts to be bought, ordered, changed, adjusted, tweaked, tuned, and such. Only if you have the keys to the Summit warehouse and do the job in there could you ever get it just right i a weekend.