Problem is different peoples accountants tell them different things.
The problem is that there is no "right" answer to your questions. There are many gray areas in the tax code, and you are in the middle of one. Until someone with the same business you're in gets audited, or gets a private letter ruling answering some of these questions, there is no way to know exactly how the IRS is going to interpret the law. Some accountants and taxpayers are very aggressive about taking every deduction they can imagine, hoping that either they never get audited or that the IRS takes a very lenient view if they do. These people might find themselves owing extra tax and penalties at some point. Others are more conservative and would rather play it safe so their clients don't end up owing money to the IRS in the future, but they also might end up paying more tax than they really owe.
I think that your accountant has concluded that your primary place of business is your home, and the clinics you visit are temporary work locations, therefore your mileage is business travel rather than commuting and is deductible.
Internet and phone costs -- as others have said, you have to pro-rate these services. However, some people argue that it shouldn't just be based on the number of minutes you spend on business calls vs personal calls. If you need to have your phone turned on so that you can receive a business call, then that entire time might be considered business use, even if the call only takes a couple of minutes once you get it. Also if you are spending time at a hospital for business purposes and using the phone to entertain yourself while you're there, then you might count that time as business use.
Per diem is complicated. Self-employed individuals can claim the GSA per diem rates for M&IE (Meals and Incidental Expenses) only, not for lodging. I am not sure how much of the rules are codified by the IRS for everyone vs by DoD and other government departments for their own employees; but I would think that if you were following the same rules government employees use, then you'd probably be o.k. in an audit. The rules I had to follow as a government contractor were:
- travel has to be 50 miles from your primary work location
- if a meal is provided on one of the middle days of a multi-day trip, you subtract that meal from your expense claim. The amount to subtract varies by meal and location and you can look it up at gsa.gov/perdiem. For Wash DC, per diem for M&IE is currently $18/$20/$36/$5 for B/L/D/IE. So, if you stay in a hotel that provides "free" breakfast, you subtract $18 per day. However, if there's no meal provided and you choose not to buy your own (i.e. you voluntarily skip breakfast and nobody offered you a free one), you do get to claim the $18.
- there are special rules for the first and last day of travel. You always get 75% of the per diem and you don't subtract provided meals on those days.
I suspect that some of your colleagues are stretching their claims beyond what the IRS would find to be reasonable, but also that you may be able to claim more than you are and not have it disallowed by the IRS should they ever look at your return.