***PLEASE HELP***1995 Jeep Wrangler

I have a 95 Jeep Wrangler Rio Grande 4 cylinder, 2.5L. I never experienced any real problems until last year. My Jeep has a little over 101,000 miles and is a stick shift. When I would drive it began to lose power like it was going to completely stop and even do like little hiccups. It would also sound like there was rattling like something was coming undone underneath and going to just fall out. This scared me so I stopped driving it and considered selling. However, I do love my Jeep and after letting it sit for over a year and driving my brothers car I decided to try to figure out the problem. I never have a problem getting her going she cranks right up and drives fine, its just I never know after driving for a period of time when this weird problem will kick in. I took it to get smogged and it passed but it was brought to my attention that one of the readings was high (AMS Emission Test Results under NO (PPM) stated MAX reading is 539 @ 15mph & 554 @ 25mph; my Jeep read 512 @ 15 mph & 352 @ 25mph). I explained to the lady at the desk the problems I'd been having and she stated that it sounded like I needed the catalytic converter replaced and referred a shop. I took it to the shop today and after they removed the catalytic converter and looked at it they said it was fine and welded it back on. The only problem they could tell me they noticed (since they had no way of diagnosing) was that I had a leaky exhaust manifold which they stated would not contribute to the problems I was having. They suggested that I take it for a diagnostic test. I came home and phoned the dealership I purchased the Jeep from and they quoted me $175 for the diagnostic test. I know this is very expensive so I decided that I would shop around for a cheaper price but in the meantime I would look online for some advice. Please help if you have any idea of what the problem could be. It has been less than 3 years that my dad replaced the water pump and last year he replaced spark plugs and the fuel filter. I am hoping this is not an engine problem that is going to cost me an extreme amount of money--hoping it is something my dad or brother can fix. Eagerly awaiting your reply.