This isn't an easy question to answer, and the best answers will be subject to debate. I'm no expert, but let's start with what we know.
1) Companies assigned to the 40th Mississippi Regiment organized over a year after the war began. Nearly all the men who later became members of this regiment were home with their families during the Battle of Shiloh, wearing comfortable civilian clothing. Only a few had been in service earlier, during the era of distinctive military uniforms.
2) State and Confederate government resources to provide distinctive or even "regulation" uniforms for soldiers were quite limited, in some cases non-existent. During 1861, the era of distinctive military uniforms, wealthy patrons sometimes paid for uniforms, arms and equipment for a company or even a regiment. The blockade had just been declared and commerce still moved in and out of Southern ports easily. Actual numbers of volunteers were relatively small, so individual communities could provide clothing for their men and raise money to purchase items like the bugles you mentioned.
By April 1862 the resources available to people at home had been depleted. The blockade tightened and prices for finished materials began to rise. Items which once adorned kepis like brass bugles and lettering disappeared. Officers attempting to recruit and organize new commands begged for arms from the government, but muskets from state armories had long since been issued, and the Confederacy awaited shipments from Europe to supply the need.
3) Companies assigned to the 40th Mississippi Regiment entered service as part of a surge of recruiting which began in March 1862. On April 16, 1862, Congress passed a law required most free white men to enroll in Confederate military service for three years or the war. The sharp rise in numbers seriously complicated efforts to supply soldiers with arms, equipment, uniforms -- even food and payments. With so many men in the army, women and other folks at home had to do the work they left behind. Demands on their time and resources made it quite difficult to provide items of clothing for soldiers. They often did, making great sacrifices to do so, but "special orders" often remained unfilled.
4) Uniforms worn by soldiers in actual service wear out quickly and must be replaced. Soldiers frequently mention holes and tears in their uniforms, and remarks about nakedness are not made in jest. Poorly-made clothing would come apart at the seams, and holes and tears might appear in places that left some men, well, exposed.
5) By the time the 40th Mississippi entered service, the ability to glance at a common soldier and guess his unit designation accurately would have been remarkable, even uncanny. Soldiers loved to gamble, and anyone who had this extraordinary skill could have won a lot of money (and made a lot his comrades angry).
6) Confederate and even state governments eventually secured contracts with manufacturers. Under contract many of the suppliers provided standard-issue uniforms and equipment for the Confederate army. These varied in style, cut and color, and were issued by quartermasters from specific depots. These depot issues provided the greater share of Confederate uniforms from late 1862 until the end of the war. Individual soldiers also wore items from home as well as captured clothing to suit their personal taste.
7) As you can see, uniforms were often anything but uniform, and standards changed frequently depending on prevailing circumstances. To get a real idea of what soldiers wore in the field, it's quite helpful to study images taken of Confederate prisoners-of-war and Confederate dead on the battlefields. Authentic images of Confederates in field service other than these are rare as hen's teeth.
Finally, the 40th Mississippi first served in General Van Dorn's Army of the West and went into battle for the first time at Iuka MS on Sept. 19, 1862. This post includes an observer's description of that little army on the march towards Iuka --