I've got two Trace TM-48s charge monitors w/o the remote functions. Reading on the Link-1000's it shows they've done some interesting things.
Finishing charge above 90% takes multiples of the time it took to reach 90% - that last 10% comes at a steep energy price but that is where the chemistry of the lead plates is healed. On a flooded lead-acid battery actually obtaining 100% charge is kind of theoretical since the minute after removing current its fallen back, 98% plus is good enough for Government work..
About the winky green LED (Q #1) there is a clarification in the FAQ's
Manual: If your system’s charging current does not fall below 2% of battery capacity at the end of the charging cycle (that is, when the battery should be full), you will need to change the Charged Current Percentage setting. (A fully charged battery is indicated when the green LED flashes on the BATTERY STATUS light bar.)
FAQ: The flashing green light is not an indicator of a full battery. It is an indication that the computer has recalculated charge efficiency. A cycle of greater than 10% of the battery capacity is required for recalculation of the charge efficiency factor and the flashing green lights. The other conditions required for recalculation of charge efficiency and the flashing of the LEDs include: 1. Charged voltage above the set point, 2. Charged current below the set point, 3. Kilowatt hours removed and returned, 4. Above conditions met for three to five minutes if alternative energy protocol not selected.
Question #2 - the 255 display might* be "The time remaining in your battery before it is completely discharged" ... 255 is the largest number of hours the unit can display...
Question #5 - If* you've got the Links' logic dialed in with the advanced settings done correctly you very well could see 220AH 'used' on the display just before the battery imploded into a mini black hole singularity and vanished from our time-space continuum... Just kidding about the implosion but yes its possible,
The rest of your questions I'd have to have a unit ticking along somewhere nearby to answer...
I like the battery box you fabricated pictured in your photo gallery - you got a control panel or inverter & woring area you could picture other than the remote link-1000?