Two things going on over the course of fitting the engine in so far:
1) I swapped to a different set of manifolds. The first set was for a Nissan 240SX and fit a bit better on the non-turbo side, but tucked the turbo a bit too far back on the passenger side. The next set if so a Fox-body Mustang, and while there was a slight issue or two on the passenger side, nothing hard to fix. And the turbo sits a few inches further forward on the passenger side.
2) My H3 Alpha motor came with a driver's side motor mount on a metal bracket that repositioned the otherwise normal motor mount 1 1/4 inches further back. I initially set the motor in my car with the STS mounts directly on the block. And after a while pondering and looking at it, I just decided to avoid various fit issues* by moving the motor forward a bit. The Hooker oil pan had about 1 1/2 inch room to move forward, and I had this neat factory bracket for the driver's side that moved it forward 11 1/4 inch, and GM has a funny way of making things that have symmetrical bolt patterns that swap side to side and even upside down with no real issue, so I just got another bracket for the passenger side. I had to do a little light grinding here and there to fit it in properly. And between both metal plates, it widens the 'stance' of the STS mounts, so I had to drill a second set of holes for them in the crossmember, about 3/8" over on the passenger side (so the motor is moved to that side by roughly half that distance).
* - clearance issues solved by moving the motor forward:
- Bellhousing/trans tunnel. This would have required a fair amount of BFH work to fit the LS1 bellhousing in. Moving it forward places the tunnel opening further along the bellhousing taper, no hammering needed at all. In the original position, that center top bolt and the way the bellhousing rises to meet it was the main issue. I also pondered getting a much more compact steel bellhousing, which would have the side benefit of catching an exploding flywheel.
- Left side header/steering column. The headers I'm using are pretty compact, but not quite as compact as a flipped cast iron header. I already replaced the rubber isolated thick steering column with a plain metal tube, but it was going to take some more work to make it fit still. Moving it forward a bit, no problem.
- CD009 (actually JK40C) transmission - This is a long transmission. And it's wide way far back along the case, where the 240 tunnel starts tapering in. Even with it moved forward t e 1 1/4 inches I had to do a fair amount of BFH work in the tunnel, making room for the wide joint in the case, and the large 'bolts' where the shifter mechanism spring detent mechanisms are at the end. Not particularly noticeable from inside the car, but still, a lot of hammering going on underneath. If the engine was still sitting back, it would have needed a LOT more hammering, making the same width out of an even narrower part of the tunnel. On the plus side, the top mount shifter (the one I'm still waiting on) probably owuld have fit into the stock shifter opening a little better, as is it will need to reach back a couple of inches.
- downpipe clearance - there's not a whole lot of room for a 3" DP, but with the motor moved forward it just sort of snakes it's way on through without touching anything, and without bashing anything. Even with a stock cheap large starter.