Current Status is:
I can start the bike on first try, it runs, throttle response is good, idle is acceptable, little low, but doesn't die. I have not rode it out of the garage. That is where the good news ends. I do still have codes and an engine light (codes 24,25,35,16,41)
(front coil, rear coil, tach, bat volt, crank sensor) I have installed new: coil, wires, plugs and crank sensor)
Here's were it gets bad. When I shut it off after the first start the next start is very hard. Turns over fine, but takes so long to get it to fire. During which I get backfire through the exhaust and wheezing on the intake. Similar to the original problem if I let it sit for a period of time, hour or so. I can go back to a great first start, but as soon as I shut it off, subsequent starts are near impossible. Plugs are both fouled black.
The second part of the testing I was trying to accomplish was just trying to see if any wires had a short to ground, that I could not see after visual inpection. So my thought was to connect the meter to ground and start touching connections that should not be ground to see if I would get a beep. I just happened to notice a reading on the meter at one point. And yes when the switch is off or the relay is out, I do not get a reading. I was not using the readings for any diagnostics, I was just listening for continuity beeps when I saw something on the display.
Thanks for the info on the meter readings. What I was trying to accomplish with in the diode setting was just continuity. I put the meter on both ends of a connection and worked the wires back and for listening for the "beeping" to stop, to see if I had a break in the wires inside the insulation that I could not see. These tests all went well, I did not find any wires that had apparent breaks in them.
So this is kind of where I am at right now.
1.) The bikes starts on first try, runs decent in the garage, have not road tested.
2.) If I shut it off, restarts are almost impossible unless I let it sit for at least an hour
3.) Will not Start at all with my PCIII installed (it's ether blown or does not like what's going on currently)
4.) Checked for shorts (checked for broken Injector wire)
5.) New Coil, wires, plugs (although plugs are fouled black now, I clean them during testing)
6.) New Crank Pos sensor
7.) New in tank Fuel supply (was showing signs of tank rub, but had not rubbed through)
8.) New Voltage Regulator (had a previous wire repair that I did not like)
9.) Voltage is 13.6-8 (as high as 14) at high RPM, 13.0-13.2 at idle
9.) Engine Light is lit with codes (24,25,16,35,41)
10.) New Start\Stop switch and Bank Angle Sensor (because I had it from prev owner)(triple checked for pinches)
I did get my hands on a used ECM with exact same P/N, I am going to try that next, I just wanted to do one more check for shorts before installing it.
Other things on my mind: Cam Sensor, Eng Temp Sensor
Things that have been corrected since the original problem:
Fuel Pump works all the time, every time.
I hate to give up, but maybe it's time for Scanalyzer or Road Tech,
just heard so many horror stories about taking these issues to the dealer.