I think this is what you should do, but I might be off.
(I have assumed an Auto Increment ID for all tables)
This is the easy part, appending the values from
insert into Master1 (SrNo) select SrNo from Master2;
Then I think you should actually delete all rows in Trans1 and then insert new ones.
delete from Trans1;
insert into Trans1 (Master1_MasterID) select MasterID from Master1;
The reason is that the values in table Trans2 has no meaning anymore, so no point in merging Trans1 and Trans2.
As I said, maybe I am totally off here and think to simple.