The 3500 uses the GM Metric bell housing Pattern. All the RWD engines in the LS family use the old SBC/BBC bell housing pattern. Only the FWD LS4 has the same metric bell housing pattern as the 3500.
Manual transmissions with the metric bell housing include: 4 speed muncie, 5 speed isuzu, 5 speed 282 getrag, 92-94 HTOB 282 getrag, 284 5 speed getrag, F23 5 speed, F40 6 speed... and a few others.
Without an adapter plate any one of these transmission could bolt up to both the 3500 or the LS4. The challenge is the LS4 does not have a starter provision and none of the transmissions listed have an OEM provision for mounting the starter on the transmission side. It is possible to fabricate a bolt on starter mount for the LS4. Once past the starter, then you need a custom flywheel.
With an adapter plate any one of these transmission could bolt up to both the 3500 (no adapter plate) or any of the RWD LS engines (with adapter plate, custom starter mount, flywheel, etc). V8 Archie sells the kit to use a metric bell housing transmission with the RWD LS engines.
For example F40 6 speed transmission has been installed behind a 2.8, 3.4TDC (nearing completion), 3800, 3900, 4.9L, N*, LS4, and many RWD LS engines using Archie's kit.
[This message has been edited by fieroguru (edited 09-11-2013).]