Mark,
A very fascinating post. I like to sink my teeth into just such a project. I spent a good part of the morning pouring through Volume 2 of the Roster and Record of Iowa Soldiers in the War of the Rebellion.
A few thoughts for you:
1. According to the ROH there are 9 soldiers from the 14th Iowa known to buried in the Shiloh Cemetery. Aleaxander Cheney, William Edwards, Chauncey Gillett, William Kyle, William Weaver, James Welch, James Williford, Edward Cayner and Isaac Walker. NONE of these men died during the battle.
2. There are 8 men that died during the battle. William Creedon, Elias Eagles, Thomas Gravett, Samuel Jenks, Samuel Lane, Samuel Lockman, William Rolan and Francis Zike. None of these men are listed in the ROH or are in known burial plots at the Shiloh Cemetery.
3. Even if were possible to determine if another soldier was in the grave noted in the ROH to be Isaac Walker it would be impossible to "re-identify" the grave. Walker's name appears in the ROH on page 177 in the section noting "Names of the Deceased Union Soldiers known to be Listed in the Shiloh National Cemetery, at Pittsburg Landing, Tenn., and Classed with the Unknown Dead." The stone in the photo on the park website is the typical marker for an unknown grave. Walker's actual burial site is not known.
4. The 8 soldiers killed in battle are most probably inside the walls of the National Cemetery resting in unknown graves. After the battle the Union dead were buried by members of their own regiments in common burials on the battlefield. Because of this most of the Uniod dead at Shiloh were identified with makeshift headboards. When the Union dead were reinterred to the new National Cemetery in 1866 most were identified as long as the markers were still legible. Because of the large number of casualties in the 14th Iowa it is possible that another regiment conducted thier burials and this is why none of the 8 are identified.
5. You are correct that neither of the Isaac Walker's listed in the roster note that they were in Company E. There was however a Zachariah Walker in Company E. This soldier was discharged for disability April 2, 1862 at Pittsburg Landing, Tn. It is merely supposition on my part but it is a likely scenario that Zach Walker died of his disability in Savannah, Tn and was buried in that town and reinterred in 1866 with the rest of the Union dead. Is it possible he was mis-identified? The vast majority of the regiment had been captured or wounded during the battle and it is quite posssible for a soldier to fall through the cracks of goverment records.

Tom Parson, Park Ranger
Corinth Civil War Interpretive Center
Shiloh National Military Park