slic3r dual extruder configuration

I finally got my autolift nozzles and am happy to report they work great...when they work. It isn't the nozzles fault though. It's my autotuning of the hot ends and improper start code in slic3r. Can anyone help me?

Print starts and 2nd nozzle isn't even turning on due to nothing queuing it up in the "start g-code" section.
When I manually set the temperature for it to start printing the nozzles drop in temperature randomly and takes a while to heat back up again. By that time the print has already failed.

Can anyone help me with autotune pid for dual nozzle setup and the start gcode commands or just tell me what I'm missing here?

Edit - Start g-code figured out. Temperatures still fluctuate a lot.
Follow instructions here:

You'll need Repetier-Host on your PC set to expert mode and have the printer connected to a computer. It's also available for Mac.

Tuning only occurs for one nozzle and the settings carry for all the hotends. Since they are identical, this is fine.

If you're only printing a single material object then only your primary nozzle will heat up. You'll need to set a toolchange to E0, heat up, toolchange to E1, heatup to the start gcode. Did you use that or another way?
Yeah, I have done exactly that and it wasn't working well. Would there be different tuning parameters with one nozzle already hot or heating concurrently?

Edit: Current settings
#define DEFAULT_Kp 10.00
#define DEFAULT_Ki 0.26
#define DEFAULT_Kd 97.75
I'll tune my latest E3D extruder right now and get back with my PID values in my next response.

When you say the print fails, are we talking about an extruder jam or a MINTEMP error (noted on the bottom line of the LCD) or something else?
Print temp drops to 186 from the set 200 with no fans on that might cool down the nozzle. There is the stock fan that cools the heatsink but it's on regardless.

edit: 650w PSU with three 12v rails at 22a each is what I'm using.
Probably affected by ambient temperatures and whatnot. Go back to the default values in Marlin. Download the original firmware and dig around the Configuration.h file.

Although I'm sure it was unintentionally, you didn't answer my question:

Is there an error when the temp falls? Something like MINTEMP or cold extrusion prevented.
OR, did you kill the print before anything like that happened.

Since this has happened to me once (The control board was running without a fan and I'm pretty sure the MOSFET overheated) - once the hotend dropped below (170 - 190 degrees) printing stopped and I got an error.
There was no MINTEMP error but the drop in temperature made the extruder start to click because it can't force the filament through the nozzle.