Are there any differences between MacPro4,1 2009 and MacPro5,1 2010 besides firmware?
The Mactracker app (for Mac and iOS) is a great resource for questions like this. You can check out all the specs for yourself side by side, but the more significant differences are:

4,1:

Processor:          Intel Xeon 3500 or 5500 series ("Bloomfield, Gainestown")
Graphics Card:      NVIDIA GeForce GT 120 or ATI Radeon HD 4870
Graphics Memory:    512 MB GDDR3 (GeForce GT 120) or 512 MB GDDR5
                    (Radeon HD 4870)
Display Connection: 1 - Mini DisplayPort and 1 - dual-link DVI




5,1:

Processor:          Intel Xeon W3530, W3565, W3680, E5620, 
                    X5650, or X5670 ("Bloomfield, Westmere,
                    Gulftown")
Graphics Card:      ATI Radeon HD 5770 or ATI Radeon HD 5870
Graphics Memory:    1 GB GDDR5
Display Connection: 2 - Mini DisplayPort and 1 - dual-link DVI