My tuner and I are having trouble tuning my swap. It's a 2003 LQ4 6.0 out of a 2003 Express 3500 Van, mated to a T56, in a BMW.

Mild breathing mods including stock CTS-V gen 1 iron manifolds, custom dual 3" catless exhaust with x-pipe, twin cutouts, LS6 intake manifold, 4" aluminum intake tube with LS7 card MAF.
Cam is a TSP 228R. 228/228, .588/.588, 112LSA. Throttle body is cable driven.
Heads are stock 317s shaved down .026" to give CR of about 10.4:1 or so. 66cc chambers.

If it matters the T56 is a stage 2 rebuild with a lightweight 18lb flywheel

We are having some very severe idle bounce even after significant tuning on his part of the fuel tables and air (MAF) scaling. The Express PCM was originally mail order tuned by Speed Inc, then tuned by my guy in May of 2013, and now that I swapped the cam we are attempting to tune again.

Rather than modify a tune that has obviously seen many changes from stock, is it possible to just flash on an LS1 GTO OS that has e-fan support, IAC support, 6 speed-friendly, more resolution in timing tables at idle, etc?

If it's not possible to flash a GTO OS the other idea was to flash just a stock Express van tune (minus all the specifics to my swap like Tach calibration, enabling electric fan control, etc) and start tuning from scratch.