You'll overcome it once you start to understand how words are built.
Obviously, as much of Persian vocabulary was taken from a number of languages, the task is quite daunting.
If you're really having a hard time guessing how things are pronounced and feel it is hampering your learning, then by all mean spend some time on formal lexical study. It will prove very useful for the later stages of your studies.
I remember when I started reading short news articles on the BBC Persian website, I was always struggling with compound nouns and adjectives.
Arabic roots have their fair share of quirks and intricacies, but if you put in some effort they definitely shouldn't be too hard to tame.
Take the arabic nouns starting with an alef
for instance. I was always reading them wrong until I realized that irregular plurals usually take a fatheh
(اَسرار : asrâr - mysteries), while verbal nouns need a kasreh
(اِصرار : esrâr - insistence). Most of the time you can readily infer from context wether the word in question is a plural or an abstract verbal noun.
Get your hands on a good reference grammar. Both Lambton and Mace have dense sections dealing with word building (moreso the former than the latter though). If you want something free, then I can only praise Philott's Higher Persian Grammar
. There's nothing more comprehensive on the market.
No need to worry though. I'd say it's normal if you have the impression to hit a brick wall when you try to read native material on your own. Vocabulary acquisition and a conscious study of grammar will eventually solve the problem.