Why don't the torque converter bolts line up with the flexplate on an LS/4L60E swap?

Almost always the flexplate and converter use different bolt patterns. The LS uses one flexplate size (168 teeth, 14 in) but different converter bolt circles depending on the transmission it came with:

Transmission	Converter bolt pattern
4L60E, 4L65E, 4L70E	11.062 in (sometimes listed as 11 or 11.08 in)
4L80E, TH400	11.5 in
Powerglide, TH350, 700R4	10.75 in

Common causes:

• 4L60E converter on a flexplate from a 4L80E engine (11.062 vs 11.5 in), or the reverse.
• An older (non-LS) converter with the 10.75 in pattern on an LS 4L60E flexplate.
• A 2009+ engine with an 8-bolt crank (9-bolt on the LS9) wearing a flexplate made for the older 6-bolt crank.

Measure the converter's bolt circle, confirm your crank's bolt count, then order the flexplate to match. Dual-pattern flexplates exist for mixing older GM transmissions.