Can you refinance a modified loan ?
As some others have stated it may be possible. It depends on your situation at the time of the modification and how the account is being reported to the bureaus. I would be happy to look into your options. Plese contact me at 651-209-2938. Jim Peterson NMLS # 695811

is it unusual to have totally different credit scores from experian, equifax & transunion?
Most mortgage companies pull a three bureau report and we use the middle score so you should be fine. Whoever pulled the report should be able to look at it and see why they are reporting a score that much less than the other two.

gross or net income considered for mortgage
To determine your debt to income ratio we use gross income. I would be happy to answer any other questions you may have. I am located in the twin cities and can be reached at 612-581-3178. Thank you. Jim Peterson. NMLS# 695811