Phosphoenolpyruvate (PEP) is an intermediate in glycolysis, not the citric acid cycle. PEP is the product of the ninth reaction in glycolysis, which involves the enolase-catalyzed conversion of 2-phosphoglycerate into PEP. All other molecules are indeed intermediates in the citric acid cycle.

The three-carbon molecule pyruvate produced from glycolysis is converted to the two-carbon molecule acetyl-coenzyme A (acetyl-CoA). This is carried out by a combination of three enzymes collectively known as the pyruvate dehydrogenase complex. The conversion of pyruvate to acetyl-CoA produces one . Acetyl-CoA has one less carbon than pyruvate; this third carbon from pyruvate was lost as carbon dioxide during its conversion to acetyl-CoA via the pyruvate dehydrogenase complex.

The citric acid cycle begins when a four-carbon molecule, oxaloacetate combines with acetyl-CoA (a two carbon molecule) to produce the six-carbon molecule citrate. The enzyme citrate synthase carries out this reaction. Citrate then becomes the six-carbon molecule cis-aconitate via catalysis by aconitase. The same enzyme then converts cis-aconitate to isocitrate, which is an isomer of citrate.

Thiamine (B1) acts as a cofactor to enable pyruvate dehydrogenase to convert pyruvate from glycolysis into acetyl-CoA so it can enter the citric acid cycle. 

Oxaloacetate combines with acetyl-CoA to form citrate. This is the first stage of the citric acid cycle. Eventually, citrate will lose two molecules of  to regenerate the four-carbon molecule oxaloacetate.

During strenuous exercise, GLUT4 will be active to bring glucose into the cell. Glucose is then pushed through glycolysis to generate pyruvate. Pyruvate is then pushed through pyruvate dehydrogenase complex, where it is converted into acetyl-CoA, which feeds into the Krebs cycle (assuming aerobic conditions) to generate ATP, NADH, , and carbon dioxide.  

Most of the intermediate molecules in the Krebs cycle can, rather than continuing through the cycle itself, go through other pathways to form macromolecules. Citrate can be used to create fatty acids and sterols. Alph-ketoglutarate can be used to make some of the amino acids. Succinyl-CoA can be used to make porphyrins, heme, and chlorophyll. Aspartate can be used to make some of the amino acids. Oxaloacetate can be used in gluconeogenesis to create glucose.

The citric acid cycle intermediate, fumarate, contains four atoms of carbon.

As a frame of reference, one molecule of glucose, the starting material for glycolysis, contains six atoms of carbon. The carbohydrate products of glycolysis are two molecules of pyruvate, with one molecule of pyruvate containing three atoms of carbon.

In preparation for entering the citric acid cycle, pyruvate loses one molecule of carbon dioxide, and therefore one molecule of carbon, to form acetyl-CoA, which contains two atoms of carbon. Acetyl-CoA is then combined with a molecule of oxaloacetate, which contains four atoms of carbon, to produce a molecule of citrate, which contains six atoms of carbon, and is the starting point for the citric acid cycle.

Citrate undergoes a number of a reactions, via the citric acid cycle, most notably two reactions in which a single molecule of carbon dioxide, and therefore carbon, is lost, thereby decreasing the total number of carbons to four atoms. The two reactions that remove carbons are the conversion of isocitrate to alpha-ketoglutarate and the conversion of alpha-ketoglutarate to succinyl-CoA. No additional carbons are removed prior to the production of fumarate, and therefore, fumarate contains four atoms of carbon. 

The citric acid cycle intermediate, malate, contains four atoms of carbon.

A single glucose molecule, which is the starting material for glycolysis, contains six carbon atoms. Glycolysis produces two pyruvate molecules, and one pyruvate molecule contains three carbon atoms.

Prior to entering the citric acid cycle, pyruvate loses one carbon dioxide molecule (e.g. one carbon atom), forming acetyl-CoA, which contains two carbon atoms. Acetyl-CoA then combines with one oxaloacetate molecule, a four-carbon molecule, to produce a molecule of citrate, which contains six carbon atoms, and is the starting material for the citric acid cycle.

Citrate undergoes a number of a reactions in the citric acid cycle, including two reactions where one atom of carbon dioxide (e.g. carbon) is lost, which decreases the total number of carbons to four atoms. The two reactions that remove carbons are the conversion of isocitrate to alpha-ketoglutarate and the conversion of alpha-ketoglutarate to succinyl-CoA. No additional carbons are removed prior to the production of malate. Therefore, malate contains four atoms of carbon.