You may already be using all the tools mentioned here and my suggestions may seem obvious, but since you asked, I will try to be specific. I can only beg your forgiveness in advance.
The most commonly used tool to link names and military service records will be the NPS index. You can use the regimental link to review names found in service records of a single command, such as Parsons' Texas Cavalry. Use only the first initial for the soldier's first name; i.e., 'J' for John and 'W' for William. Possibile matches will be missed by searches based on full names.
http://www.itd.nps.gov/cwss/
To eliminate objections to your unit ID for Mr. Gilbert, use Ancestry or a similar tool to place him in a state and county during the war. The 1860 census ought to prove useful in that regard. Unless he remarried, the name on the widow's pension application should match that given on the census. Place her on the census close to the date of application, using name, age and place of birth. Now you should have a positive ID for the veteran and his widow.
Next you need to identify your Captain Scott. There are two or three ways to accomplish this. Using the NPS index, you could check every Scott who served in a unit from the same state, making notes about any company officers by that name. Sometimes veterans would mention lieutenants at the higher rank of captain. That should leave you with a small number for further review, maybe just one. Now check for men named Gilbert who served in their command. Hopefully there's one match.
To confirm your identification, Mr. Gilbert and his commanding officer should be from the same part of the state. Perhaps both of them are residents of the same county or adjacent counties. That should leave you with a reasonable identification and a strong feeling of a job well done. If you have questions, post an inquiry here for experts knowing more about the regiment, battalion or company you've identified.
People make improper unit IDs based on a name/state link every day, and that falls short of our goal of honoring veterans properly. Responsible organizations should be aware of this and raise questions about any purported military service. Substantial evidence should be available in most cases.
Let me know if you have other questions. I liked your web page on CSA burials. Do you have a source for the article on C. C. Crews?