Have neither SPF or 428, but do have some thoughts on just this having done install in 351W/T-5 with same issues.
On one hand, it's easier to squeeze the motor in without the trans, then install the trans from the bottom. And on any other normal sized car this might be the best approach. But on a Cobra, there's hardly any room to work. So if you want to install the trans onto the engine with all the alignment nonsense you have to go through, put the package together on the shop floor. Then install as an assembly.
The way we did it. There must be enough room under the chassis for the engine hoist to roll. Car frame must be supported solid, not on the front suspension. You may need to extend the reach of the upper hoist arm. It's close, and the hoist may hit the nose of the car. Put a blanket, pad, or mattress against car nose.
You absolutely must have an engine tilter for the next manuver. Point the crank handle toward the back of the car, or you won't be able to turn the crank at full tilt. Install trans dry, or with tailshaft plugged with a tailshaft plug, and taped. If not, you'll have a garage floor full of trans fluid. And have a few buddies to help. Don't try this on your own, particularly with an FE.
Lift assembly with hoist until pan clears nose. Slowly manuver engine rearwards. Start tilting trans end down. Put a creeper on the floor to support trans off floor, and help it move under car.
At this point, engine and trans are hanging by front two bolts, and trans is resting on creeper. Engine moves down while trans moves back.
Oil pan, and then water pump come close to car nose. Remove, and install later if it won't clear.
As motor mounts get near frame mounts, slide screwdrivers through bolt holes to help alignment as engine moves down.
Jack trans up so engine levels out. Might want to install trans mount loosly to keep engine level.
Before resting engine weight on frame, use the screwdrivers to move engine to position bolt holes. Get at least one bolt in per side. Take screwdrivers out and get the other bolts in. Drop engine, disconnect hoist, and snug up. Put headers and sidepipes on hand tight. Sidepipes level with car? If not, need to shim motor, or trans.
Can you get to trans fill plugs? Can you get to trans shifter bolts? Can you install starter? etc. etc. Once everything is in, and lines up, snug it down.
Got a close look at SPF motor to frame mounts at DVSF. Looks a little thin!? Reinforce with 3/16" or 1/4" plate before installing engine??? Same for trans???
Would install Canton road race
oil pan, and crank windage tray on any engine going into a Cobra. FE no exception. These things just corner too well to risk loss of
oil pressure.