I like option 2 only without the wild card teams.
Each of the quarter winners would bowl against each other as a whole and not as separate pairs. Have the teams move to where each team will bowl 1 game against the other 3 never bowling on the same lane. I am showing all 16 teams to show the movement.
Example
Lanes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Game 1 Q1 Q2 Q3 Q4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15 T16
Game 2 T13 T15 T14 T16 Q1 Q3 Q2 Q4 T5 T7 T6 T8 T9 T11 T10 T12
Game 3 T9 T12 T10 T11 T13 T16 T14 T15 Q1 Q4 Q2 Q3 T5 T8 T6 T7
Q# = Quarter winners
T# = Team positions for non Q winners
I think it would be best to use a team handicap system, where the high average team in each block would be giving pins to each of the other teams.
Hypothetical numbers.
Q1 1100
Q2 1080 (20*.8) +16
Q3 1060 (40*.8) +32
Q4 1040 (60*.8) +48
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