I have a very close friend in the train store business. What Lionel Grandpa and Carl Orton suggested is very good sound advise. Follow it first.
Your plan to have Thomas is a sound one as my friend does the same. At times Thomas carries the store at other times the O gauge. However, his store is combined with selling & repairing an entirely different product.
During the summer months things could get very slow for trains. During the holiday season things could get hectic and at times unnerving as Lionel and MTH are at times late with delivering their Christmas merchandise for the holiday season. If they mess up and you miss that window when people are walking about the store. You'll be holding those items until the following season.
The discount you have from the authorized distributor is not the best as your online competition can at times sell it at your cost or less! The mixture of trains like HO is helpful as it will draw in some business. Keep in mind HO represents 80% of the train hobbyists. The remaining balance of 20% consists of N, O, O scale, G Gauge etc.
In order to get a distributor to sell you trains, Lionel must approve of you first. This will include having an onsite inspection of your store looking for a in store operating layout, adequate Merchandise (purchased at retail prices!) and checking to make sure your store location isn't too close to another retailer. All of this costs money.
My friend barely ekes out a living, but his shop isn't the best stocked either. He tried caring locomotives and had a very difficult time selling them as they were typically cheaper elsewhere. Over time he has learned his customer base and stocks those items that they are attracted to. He does not carry everything nor do I suggest you do the same. Some items will sit on the shelves forever. Also bear in mind local road names as they tend to do well. Obscure road names of smaller carriers (say in your case from the east coast) will rot on your shelves.
You'll need lots of track and switches, and other small items needed to maintain a modest or carpet layout. Many people simply only run their trains at Christmastime around the tree. Thus they won't need much in the way of layout scenery.
My advice would be very very very carful. Your not a spring chicken anymore and you don't have 30 yrs left to make up for any mistakes unlike someone in their 20's.
Wishing you much luck.