The results of the company's cost-cutting measures
are evident in its profits, which increased 5 percent
during the first 3 months of this year after it fell over the last two years.

(A) which increased 5 percent during the first
3 months of this year after it fell -- pronoun reference error -- it cant refer to profits

(B) which had increased 5 percent during the first
3 months of this year after it had fallen -- pronoun reference error

(C) which have increased 5 percent during the first
3 months of this year after falling -- this is the most clear and concise choice...

(D) with a 5 percent increase during the first
3 months of this year after falling -- the use of with is not appropriate here...

(E) with a 5 percent increase during the first
3 months of this year after having fallen -- same as D

IMO C

The results of the company's cost-cutting measures are evident in its profits, which increased five percent during the first three months of this year after it fell over the last two years.
a. which increased five percent during the first three months of this year after it fell -->incorrect modifier it. They is better to match profits
b. which had increased five percent during the first three months of this year after it had fallen -->...had increased ... after it had fallen... is surely ungrammatical. Besides, same error as A
c. which have increased five percent during the first three months of this year after falling -->best. The first three months is an indefinitely time and likely to last until now, so present perfect is best.
d. with a five percent increase during the first three months of this year after falling -->with + Noun phrase + after + present participle + ... is ungrammatical. Besides, it seems to modify for the results, not for profits, meaning The results have a 5% increase (???) after the result fell over the last 2 years --> awkward meaning
e. with a five percent increase during the first three months of this year after having fallen --> same errors as D