INSW20

If VE is that high at idle but looks closer to normal at higher loads then I would be most suspicious of deadtimes.  A quick test is to hold it at constant RPM about say 2000RPM and adjust the target lambda by 10%, if the deadtimes are correct then the measured lambda will also change by 10%, if not then scale the whole deadtime table up or down until measured lambda follows a target change closely.

I assume you went with the Racer X rail and their bosch regulator option -- I always advise my customers against that regulator option and just stick with a proven adjustable regulator like the Aeromotive 13109.  Yeah they cost more and you have to buy fittings and lines, etc.  They *always* work. 
A lot of your adjustments and trims are a bit... different... than I'm used to seeing and I can only guess the fuel pressure being so high is a big part of it.  Your dead times didn't match the information I have exactly from Injector dynamics website, but it wasn't far enough off to make that large of a difference.  Is your engine a Gen2?  I woudl start as a safe base of about 14 degrees of timing at 14-15psi boost (100kpa boost).  If it's 3rd gen or higher I would start a couple degrees less as a base.  

You need stable and predictable differential fuel pressure.  If you know the regulator is under sized then you need to fix that, you are not going to be able to get a a good tune when the fuel pressure is so poorly controlled.
 
 Injector flow is correctly modelled using Bernoulli's equation.  Flow change is roughly proportional to the sqaure root of the pressure change.  
 
Injector timing isnt really relevant at this stage, but just FYI, at idle and cruise with normal injectors close to the valves, the ideal EOI will usually be around 360-400BTDC.  You want the fuel to sit on the back of the hot intake valve for as long as possible to be best vapor in the port.

Yeah scopes look ok.

Typically a misfire will show as a lean spike or overall leaner running average than reality.  I've had cars run on dyno so rich they did misfire, and the AFR looked like it was spot on, lol.  I removed 15% fuel and the afr read richer without misfiring.  Rich misfire sounds like a limiter being applied usually.  

I would guess you're more likely having a trigger threshold error.  What is the arming voltage (logged) versus actual trigger1/2 values at that rpm?  Can you run a trigger test at the rpm where that was happening?

Maybe increase a bit the trigger 2 threshold. 
I will let Adam give the last word but it looks like the small hump on there may give you an error

I've had to tweak the trigger thresholds on several distributor 3SGTEs/Toyotas to get no misfire or errors at idle with the Link (which is more than I ever had to do with some other ecus).  Typically I would run a trigger scope at cranking and every 1000 rpm that there are threshold break points and then set the trigger threshold value to approximatly 1/2-2/3 of the scope peak reading at each break point.  This has worked well for me so far.

Yep, if the tank weren't already full of E85 (77%) then I would have started there.  I'll just get it as far as I can and then let the actual tuners take it from there.  Thanks!
(Also, can't thank you enough for these Spearco IC pipes!  )

I find it much simpler to tune petrol first, and once you tune whatever blend of ethanol and petrol you want, it is possible to extrapolate the 0% and 100% tables linearly in excel (assuming you use the same axis breakpoints on table 1 and 2).  

This was a customer car with a 12 position switch (AEM I think) I remote dyno tuned.  We set the swtich to allow it to blend between his minimum (pump gas) boost level and different levels on ethanol depending on switch position.  I know this isn't exactly what you were asking to do, but it shows another approach to still get proper ethanol content based boost with multiple switch positions.

The reason the switch position are on the x-axis of these boost tables was there wasn't 12 rows available on those tables

Yes you can do that.  You will need to use vitrual auxes where you want to trigger a complete change of a table, but for a lot of the functions you will probably just be able to put the switch position on the axis of the table.  
Here is how the switch would be set up, the cal table is used to convert the voltage into a "position number".  

 
And then for something like the RPM limit you could just put switch position on one axis.  Here is an example with a 7200 limit in most positions except higher limit in pos 3 and valet limit in pos 3:

 
For boost you could either do it similar to above with switch posiiton on the axis of the boost target table, or you could use virtual auxes to switch tables.  Here is an example of switching to a low boost table for position 2: