1a). Under acidic aqueous conditions:
KMnO4 → MnO2 → Mn2+
1b). Under basic aqueous conditions:
KMnO4 → MnO2 → Mn(OH)2 → Mn
Please, take a look to the above half equations and the corresponding voltages, from tables of various sources and then, you will clearly understand the role of pyridine.
2). During oxidation reaction, the oxidant is added in accordance of the oxidation number equilibrium and not at a molar ratio.
3). Thiophene oxidation steps:
Thiophene S-oxide→Thiophene S,S-dioxide→Semisuccinic-suflonic acid (HO3SCH2CH2CO2H)
4). During oxidation reaction, nitrogen containing moieties might be oxidized to the corresponding N-oxides by the excess of the oxidizing agent. However, low amounts of N-oxides side products, can be reduced by shaking with fresh iron powder or fresh zinc powder (Attention: this might be dangerous with flammable solvents (low flash point) and in absence of water}.
5). According the “good laboratory practice” and in a multi-step synthesis, a compound must be highly purified before being introduced in the next step (that makes life, easy). Especially in cases of biological and pharmaceutical interest, where the purity of the product is more important than the yield.