Yeah, sorry to go so off track from your original question but seems like you have more important issues then a air filter, lets figure it out so you can be happy with your LS swap
In order:
1. E38 - post a picture of your ECU. This is the Gen 4 ECU used from 07 and onwards, when I said they can be tricky, they have a TON of features that when working correctly make a vehicle like a 2010 Silverado work flawlessly, however once in a swap, stuff like Torque Management, abuse modes etc can get in the way. I have very little E38 experience, but I'm going to wager your best bet is to probably just have a completely new tune file uploaded and start from scratch. There are several guys that you can just mail your ECU to and it may be more convient then to try and find a local shop. Lt1swaps.com, pcmforless.com and 150tunes.com are a few that are good.
2. closed loop means that your ECU is using feedback from the O2 sensors to constantly modify the fuel mixtures to provide correct air/fuel ratios. Loop: Combustion, o2's read exhaust mixture, ECU uses that data (along with TPS, MAF, MAP, and all other sensors in harmony) and runs the engine, combustion, repeat. "open loop" means that the ECU just uses default settings and is not as efficient. Generally open loop is just for when the engine is cold and will go into closed loop once at operating temperate, I believe the default coolant temperature to enable closed loop is 185-190 ish
3. That's nice but without actually changing the tune in the ECU you aren't changing anything
4. ^ when you say "reset", and "swap", what do you mean, exactly?
Really, there is no reason not to run all the sensors in their original configuration in something like a Land Cruiser with a stock LS engine for most users. There are benefits in performance cars or with forced induction where the stock MAF sensors can only read a certain range of data and don't work properly past that. Unless you are experienced with his kind of thing and know what you want and what you're doing the best bet is to just have the engine management work the way GM intended it to. If that makes sense.