I recently purchased a copy of Steven Newton's Joseph E. Johnstonand the Defence of Richmond (amazon) - his PhD thesis.
Appendix B I found fascinating, which was an attempt to derive Johnston's actual strengths, and Newton calculates a much larger force than Johnston is typically credited with. On the Peninsula his starting point is the almost complete 30th April trimonthly field return (there should be returns for the 10th and 20th April, but they seem not to have survived). Newton notes the figure given is for "effectives" and excludes a few organisations. Using Livermore's conversion (which is simply to add back in officers usually) Newton estimates a strength on 30th April of 65,015 PFD. Given known disease rates Newton calculates Johnston arrived on the Peninsula with roughly 72,739 PFD. This is a significantly higher figure than usually supposed.
More impressive is Johnston's force at Seven Pines, which is calculated at 87,890 PFD on 31st May. With reinforcements that arrived the next day the field force would be 94,813 PFD, and this excludes the heavy artillery in the Richmond fortifications and other posts.
This makes Lee's strength of 113,282 (fn 75 to chapter 10 of Harsh, McClellan's War, referencing LW Tenney's MA thesis) during the Seven Days more credible. It always seemed odd the sudden apparent jump in strength under Lee. It now seems likely the strength increase was far more moderate.