Firstly, just to clarify the JF-17s ordered for the PN will be identical to the versions flown by the PAF, there won't be any modifications needed to be made to the JF-17 as it will be flying from shore bases so Pakistan won't need to face the "pain" of nasalising the Thunder. It is true the ADA/HAL are having some difficulties in navalising the LCA for the IN who wants to fly it off their aircraft carriers which is primarily down to the need to strength the undercarriage but not add a huge amount of extra weight (the issues with this are obvious to see). This is compounded by the fact that not only is this India's first home grown fighter but there is now the added complexity of needing to modify it for carrier operations- something only a select few countries have ever done and India is on a very steep learning curve.
Like I said, as the JF-17s for the PN will be flying from shore bases there won't need to be such modifications and additional development/testing required so you won't encounter the same "pain".