Realistically, I don't think the gap necessarily would need to come into play. I am currently awaiting final UW approval on my USDA guaranteed loan, and I have seen nothing in the eligibility requirements that indicate continuous employment as a requirement for eligibility. The requirements include income cap (specific to rural area), must not own adequate housing currently, must be able to make the mortgage payment (shown through DTI) and must have 'reasonable credit history'. And, of course, the home must be in a USDA approved area (be sure to check USDA's website or contact them. I have heard stories of some areas where a house on one side of the street qualifies and a house on the other side doesn't).
So from a USDA perspective, I don't think either of your issues (gap in employment or lack of stubs for 9/08 through 12/08) would cause an eligibility question. From the lender's perspective, they might question the 2008 income, at which point you might end up needing to disclose the gap. I was asked to provide W2s for the last 2 years (and ended up needing to provide 2007 and 2008 returns as well), and only required paystubs for the previous 2 months, so in your case, the stubs shouldn't be an issue.
I'll leave it to the experts to weigh in on how much of an issue they think a UW would have with the gap, but if you've had steady employment for all of 2009, especially since it's in the same field as your previous work, I would think it sounds promising.
Good luck.
