Top Ten Newbie Mistakes
1A) (NEW) Trying to diagnose running problems on a bike with an unknown maintenance history is an exercise in futility until a baseline is established through proper maintenance. Things like clean carbs, properly adjusted valves, sealed intake system (airbox, carb boots), a clean gas tank (no rust), and a properly functioning petcock are 100% mandatory for the bike to run properly. It's best to perform all the bikes maintenance when you first get the bike, and then if problems show up you will know what the problem is not.
1B) Incomplete carb cleaning. A proper carb cleaning requires a full tear down, soaking the parts in carb dip, and reassembly with fresh O-rings (cycleorings.com). Pilot jets, choke tubes, and pilot circuit passages in particular need a proper cleaning before the bike will run right. Even if the bike seems to run right, if the O-rings are original they are sure to be hard and brittle thus problems could be right around the corner. This is a link to a carb tutorial that you may find useful...
http://www.mtsac.edu/~cliff/storage/gs/Mikuni_BS-CV_Carburetor_Rebuild_Tutorial.pdf
2) Not replacing the intake boot O-rings. The classic "hanging idle" (or idle speed that increases on it's own as the bike warms up) is often traced to this simple fix since air gets sucked past the old O-rings and into the engine causing a lean condition. Most GS bikes have these O-ring, but not the 2nd generation 750 or 1100E family. While you are at it, make sure the entire airbox system is 100% sealed, since drawing false air into the system will increase running temperatures and make the bike run poorly.
3) Not adjusting the valves. The valves tighten with mileage, and once all the clearance is gone the valves hang open and burn. Not good. If you wait for your bike to misbehave before performing this critical maintenance, you may damage the engine. If your valves have no clearance, you will need a thin checking shim in order to properly calculate the needed shims for your engine.
4) Trying to run the bike without the airbox...or installing pods, or a header, w/o rejetting. The air/fuel ratio will be drastically lean, which will not only cause running problems, but likely damage the engine too by causing it to run hot. Installing a free flowing exhaust will likewise change the jetting requirements, but not as drastically as pods.
5) Ordering "carb kits" full of inferior aftermarket jets. A new O-ring kit from cycleorings.com is all that's necessary most of the time. Get some new float bowl gaskets and pilot jet plugs if necessary from a place like Z1 Enterprises to supplement the O-ring kit.
6) Trying to clean out the brake system full of brown gunky fluid by flushing the system. If the fluid is dark and brown the only way to clean the system is a full tear down and clean out otherwise chunks will remain behind in the system. While your at it the old rubber brake lines should be changed. Suzuki call for replacing the lines every 2 years, so if your bike still has the originals you are 28 years overdue.
The old lines will lead to spongy brake lever feel and contaminate the fresh fluid you just installed.
7) Waiting for the charging system to fail, instead of cleaning up the old wiring. Many a battery have been boiled dry after the grounds corrode. Running a dedicated ground to the battery, or a solid frame attachment point, is strongly advised. Suzuki also botched the stator wiring by routing one leg up to the now discontinued head lamp switch. This needless wire path often overheats and damages the harness in the process. Do yourself a favor and rewire your charging system: run the stator wires directly into the R/R, make sure your R/R has a solid battery or frame ground point, and run the positive (power) R/R output either straight to the battery (with 20A fuse in-line) or though the regular fuse block after you check for resistance in the circuit and repair as needed.
8) Using the wrong oil and/or gasoline. Auto oils have less zinc and phosphorus (high pressure additives) than they used to since the EPA has mandated reductions to protect catalytic converters. Motorcycle oils are fine but expensive, and even motorcycle oil has reduced additives these days. Diesel engine oil is cheap and contains lots of high pressure additives appropriate for our engines. Shell Rotella oil is even certified for use with wet clutches if that makes you more comfortable, although just about any diesel oil is fine. As for fuel, Suzuki calls for use of Regular gas. Using Premium provides no positive benefits for your bike and is more expensive.
9) Search out the information about your upcoming wrenching tasks before going off unprepared and possibly damaging something. Search using "Advanced Search" and then click "Titles Only" to quickly hone in on the topic at hand. Almost every possible question a newbie could ask have already been answered. For example: there are tons of threads on how to avoid broken exhaust bolts and float posts. Sadly, most newbies learn these tricks AFTER they damage their bike.
10) Buying a 30 year old motorcycle because it was cheap without any mechanical knowledge and no interest in learning. Paying a shop to work on your 30 year old motorcycle is not advised unless you have lots of money to spend and know for a fact that they are trustworthy.
