"I had thought there was" Vs. "I thought there was"

Solution 1:

The first form is used only when you describe event/state that happened/lasted before another event in the past. The second is just plain past.

"I had thought there was something wrong with the tape recorder until I heard my own voice recorded with studio equipment." (the thought ended when you heard it)

"I thought there was something wrong with the tape recorder."
"No, it was just a bad tape." (there were no other actions that would end your thought in the past)

Solution 2:

A great deal depends on the stress. If thought receives strong stress, then it really doesn't matter which one you say; they'll come out the same anyway.

The consonant cluster /dθ/ is very hard for English speakers to pronounce, and we tend to elide it to simply /θ/, which would delete the only mark of the past perfect auxiliary had, and make the two forms indistinguishable in ordinary speech.

I.e,

• I had thought ... would come out /ayd 'θɔt .../; /dθ/ => /θ/, producing */ay 'θɔt .../
• I thought ... would come out /ay 'θɔt .../, the same as the other one.

How you write it is up to you. Grammar is about spoken language, not writing.