Cleburne and Forrest were junior, definitely;
This may seem ASB, but what about Cleburne? I don't know if he could get top command bing Irish, but he and Forrest were the two best commanders in the west by far. At least give Cleburne a corps, I believe he would fight with it better than most.
And didn't Breckinridge turn out to be a decent division commander? He had a good record in The Shenandoah, albeit against weak opposing commanders.
FWIW, the Army of the Mississippi's organization at Shiloh was:
CG: Gen. AS Johnston
2iC: Gen. PGT Beauregard
I Corps - MG Polk; 1st Div (2 bdes) - BG Clark; 2nd Div (2 bdes) - MG Cheatham
II Corps - MG Bragg; 1st Div (3 bdes) - BG Ruggles; 2nd Div (3 bdes) - BG Withers
III Corps - MG Hardee; (3 bdes; no divisional organization)
Reserve Corps - BG Breckinridge (3 bdes, no divisional organization)
So, if Bragg is out of the picture, presumably Beauregard gets the II Corps. The overall organization is pretty weak, however; in terms of present for duty, the II Corps had ~16,300 men, but the I Corps only had 9,400, the III Corps had 6,800, and the Reserve Corps had 7,200...army level troops included a single separate infantry regiment of 700 and a cavalry force of 4,300.
A rational organization would have split the 40,000 infantry and artillery into four divisions of 10,000 each (four brigades to the division) and assigned them to (presumably) the four senior major generals: Beauregard, Bragg, Hardee, and Polk. If it were possible, maybe send Polk to the Gulf and give the fourth division to Cheatham.
If Bragg is not around for whatever reason, Polk stays and Cheatham gets the fourth division.
Best,