LY6 B1S1 Going Lean - Some Diagnostics & Log Attached

[lost honda pro]

Hi Everyone - Long time troller; first time poster. Please let me know if there's additional info that would help; I'm very new to tuning...

Background:
-'07 LY6 mated to 5-spd running OE E38 (wiring done by myself) w/ '87 C10 tank, Delco pump & vette FPR
-turned off VATS & B_S2 o2s & EVAP & extra crap (THANKS FOR ALL THE GOOD POSTS ON THIS!!)
-starts up & runs consistently (though rough; see below)

Problem:
-first started engine in bare chassis in April 2014 and both B1S1 & B1S2 were bouncing fine (log file attached)
-got it wired into the truck last week and now B1S1 starts @ 450mV (with B2S1) but slowly drops to 0mV (log file attached)

Diagnostics Done:
1. suspected bad B1 o2 sensor; swapped o2s and the problem stayed with B1 (o2 sensors both work)
2. suspected i swapped B1 & B2 as others have done; swapped harnesses side-to-side and banks did opposite rich/lean (so harnesses was correct)
3. Looked for vac leaks & found none (wouldn't a vac leak affect both banks, unless right on cylinder-manifold gasket?)

It'll run in open loop (forced) and B1/B2 injector pulses are both around 3.5-4.0 ms (as in log files), but when it warms up and I let it go into closed loop, it tries to compensate for the lean condition with B1 going up to 6.5-7.0ms. I've gotten hit/miss DTC for lean on B1.

I'm hoping there's something obvious that the more experienced tuners can point out; at this point i'm about to start tearing into the rail on B1 to check for injector debris.

Thanks in advance for any help!

[lost honda pro]

I've been changing various things and have finally made some progress:

1. Pulled plugs (they were the original 41-985). All were worn, some were black. Replaced with new OE 41-110.

2. Checked all wires with timing light. All coils are firing and and wires seems to be carrying current. No misfire DTCs.

3. More searching for VAC leak... The PCV valve/stamped fitting in the driver's valve cover goes straight to the top of the manifold - is this correct? The engine is always pulling the crankcase to intake pressures? How many of you have simply put a filter on the valve cover and capped the intake manifold port? Also, is there a small nipple on the truck manifolds for the HVAC controls? I can't find it though i've seen it referenced on many other LS manifolds...

4. Confirmed all injector wiring is correct.

5. Here's where it gets strange... I was sitting on the couch looking at the tune, trying to see if there's anything obvious I might have accidentally done. I don't know what I'm doing so nothing jumps out. I save a new copy of the tune (as I turned some additional DTCs on) and write the calibration last night. The problem *seems* to have gone away . I didn't change anything in the tune of substance, so my only guess is that the battery voltage/laptop voltage was low when I wrote the previous tune. Has anyone ever experienced a write problem like this? Does battery voltage matter THAT much?

I'm going to confirm it's running better tonight when I get to the shop. Thanks for any insight anyone can provide.

Tim