Homeowners insurance estimate does not meet estimates we got?

We had a tornado come through our neighborhood and have some damage, although not at bad as one street over from us which was pretty much demolished. We had trees uprooted and land on the corner of our house, half our fence destroyed, and other minor damage. We took pictures of everything. The insurance adjuster came out for an inspection, but the trees were still on the house so some of the damage wasn't visible. He told me to take pictures after the tree came off, get estimates, and email him all the information. He also said that because the tree is on our house, if a local company came by and offered to remove it and the price seemed reasonable, to go ahead. Well, we had a company take the tree out. It was actually three trees (insurance is counting it as one) that grew out of the same root system (two birches and an oak) and we were charged accordingly. We've also had estimates done for the fence and roof. The fence estimate was okay with our insurance, but they have problems with the roof and the cost of the tree/stump removals. My cousin and uncle own a tree removal company in another state, so when we heard the price for removing ours I called them and they both said it was a fair price. We went ahead with it. As for the roof, after the tree came off we found a few shingles missing, some with damage, a gutter that was destroyed, a hole in our siding, the cap on our chimney was ripped off, a joist broken, soffet (sp?) damage, and trim pieces missing. (There may be more, but I can't think of anything off the top of my head.) Our roof estimate includes all of those things being repaired/replaced, plus labor costs. Now our insurance doesn't wait to pay for the trees or roof because they think its too much money. We've had three estimates done for the roof, but they were for more money and didn't include repairing/replacing all of the things I have listed above. My dad, a roofer, thought the estimates were reasonable. What do I do now? Get more estimates? Take less money from insurance and wait until my husband gets back (he's Army) to have him do the work himself?