Yeah, I had that happen to me a few years ago while making a couple of roguelikes in ZXBasic. Almost ran out of memory, not to mention how slow they ended up. And that was in a compiled language! Whereas it sounds like you're trying to remake Elite in Sinclair Basic. o_o
Well, good luck. That was one of my favorite games at the time. Can't wait to play your version. Don't worry too much about the line count limit, I think it's a soft limit, and your ambitious project definitely justifies going over it.