When you say you are missing lines etc. I assume you are talking about toner on your un-etched PWB. You can get a lot of clues about what is happening by carefully examining results.
1. First, is the paper stuck to your board? It should be. If not you either didn't fuze the toner, or it didn't stick to your board. If you have a low density circuit the paper may peel easily from the board, but I haven't had much success mechanically removing the paper. Water soak and gentle abrasion if the fuzing process was successful.
2. Are the traces that ARE there easy to remove? If so your issue is adhesion and is more likely to be a cleaning/surface finish issue, but may indicate marginal fusing temperature.
3. Use a strong magnifying glass or microscope to examine the traces which did transfer. Look for clues about how the fuzing went.
4. Try test runs fuzing a pattern from one paper to another. While the thermal characteristics of the paper are very different from paper, if your heat source can't make this transfer you need something hotter, more time or something along those lines.
Everyone will have different tools available to diagnose the problems. If you are using this method your tools are likely to be crude and or makeshift (since low budget is the most common reason for doing it), but that just means that you will have to use your head more extensively.