To find the conditions for separations of your products, you can make several attempts on the eluent then you trying to make a gradient Methanol - water and on the other hand a gradient water - ACN
You need to develop a method with different combinations of solvents you have so that you get separated peaks...following article may help you to develop method...
yes, you have to standardize the ratio as well as flow for better separation according to your reference paper. The ratio may be differ from your reference may be due to your column, and system difference as well as chemical purity.