Has Ukraine responded in any way […] ?
Yes, "in some way".
Prosecutor General Yuriy Lutsenko has responded by making public his response to NYT journalists Andrew Kramer and Julia Mendel dated earlier, 20 Apr 2018 (scans of the letter available).
Which make a perfect sense: the Menendez-Durbin-Leahy letter has been inspired by the article by Kramer-Mendel @NYT.
specifically to the final 3 questions asked in there?
As per the 3 factual questions:
On 3 May, in his interview to Reuters, Lutsenko stated that the FBI hasn't responded Ukraine's requests:
Asked about progress on investigations in Ukraine relating to Manafort, Trump’s former campaign chairman, Lutsenko said he was told in autumn by the Federal Bureau of Investigation (FBI) that they had launched their own investigation and could not provide information at this stage.
Also, according to Deputy Attorney General Yevhen Yenin,
The US law enforcement — neither the FBI, nor Muller — have asked the Prosecutor General's Office (GPU) for any legal assistance in connection with the Manafort case. That is, there was no cooperation to restrict at all.
On the other hand, it should be understood that in the current political situation Ukraine would not rush to irritate Trump and his administration because Ukraine depends on the US' military aid to withstand the foreign armed invasion.
Summarizing sources listed above, the three answers seem clear:
Q1: whether his office had indeed taken steps to stop cooperating with Mueller
A1: There was no cooperation between the GPU and the Mueller probe; there was nothing to stop;
the internal GPU's investigation of Manafort's affairs in Ukraine has never been (officially) stopped;
Q2: whether anyone acting for the Trump administration had asked Ukraine to do so
A2: There was nothing to stop.
Q3: whether the Mueller probe had been raised during previous bilateral meetings between the two countries
A3: the GPU is not in position to comment the information about bilateral meetings between President Trump and President Poroshenko.