So I have finished all the required steps to transfer over to the coast guard from the navy. However my process has been put on hold due to my debt to income ratio being to high. Now this came to a surprise for me as I only have two debts which are a mortgage that I have had for over a year and a car loan that I have had for 4 years. what steps could I do to fix the situation. when they did the calculations they used E3 base pay and my home town bah but didn't take into account my time in-service 3 plus years.

Are you single? I had this same issue, minus transferring from another service. I was single and had a mortgage. I was on the fence on selling my house, until the recruiter told me for debt to income ratio on non rate pay, I'd have to sell my house. I had zero debt minus the mortgage. They said they may have been able to work around it if I had my roommates sign contracts but in the end I sold it for a profit anyways. I don't know how much truth there was to all of the statements they told me but just wanted to share my experience.

Are you planning on renting your house? If so, just show your rental income and that should clear things up. It doesn't really matter how long you have had the loans, it matters how much your loans cost. Can you pay off your car loan? If you have had it for 4 years, there shouldn't be much left on it. If you can't pay it off, another option would be to find a low interest rate and refinance it for another 60 months. That will drastically lower your payments on paper and you can still make the same payments you were making and pay it off in the same amount of time.
There isn't a huge difference in E-3 pay for time in service and it tops out at 3 years I think anyways so it won't matter if you're an E-3 with 10 years or an E-3 with 3 years. I guess it really depends on how far over the 30% debt to income ratio you are at this moment. Your best bets are to show a rental contract as income and refinance your car if you can do it without paying a higher interest rate and continue to make the same payments....or just pay the car off.

I'm married and plan on paying off my car off and that will hopefully bring me at or below 30%. I plan on renting the house out once I find my first duty station.

Depending on if your spouse works, that'll help. Looking back I wish I would have kept the house and rented it out, since I have a lot of ties to that location and visit often. The recruiters talked me out of it based on their own experience, it wasn't worth the hassle. I definitely understood where they were coming from.

My wife doesn't work right now she is a full time student finishing her degree up. I plan on just paying off my car loan depending on what my recruiter say tomorrow. I saw on the recruiter manual that there is a waiver for people that are over the 30% unless I read it wrong. I have never missed a single payment yet...

Financial waivers are available for request if there is exceptional supporting documentation and a financial plan, but still not a sure thing.  A spouses income may only be calculated if the spouse is in the military.

How hard is it to get the waiver what documents will be needed. How in-depth does the financial plan need to be? should they be using my time in service when they are calculating the debt to income ratio. I will be transferring over to the coast guard with no break in service once this finical issue is resolved.