Sounds like you have two problem. Too low engagement for the engine that is peakyer with the pipes and a higher end overrev. I am not sure were those pipes are suppose to run at but it sounds like you are saying around 8,200 rpm. Please confirm that. Unless you do something like an engagement notch (Not Recomended For Trail Use) on the weights you will never be able to get the engagement up high enough. The shims don't move it much. You have a 97 so you should have the short primary cover. Unfortunately there are no springs available from Yamaha, for that cover, that have a high preload rate. (Unless someone here knows of an aftermarket one that does). You are going to need to find a tall cover from one of the later primarys first. They bolt right on. Someone on here should have a used one you could buy. Then you can use a spring with a higher preload that is available for that cover. Looking at the old max perf catalog that somebody so nicely scanned on here. It looks to me that a
Blue-White-Blue PN 90501-583L0-00 would be a good start. The total force is nearly identical to yours and the preload is up from 35 to 45. I think you may still need to add shims to get the engagement up were you need it. This spring will probably bring your shift rpm up some as well, but you need it to be higher at take off. Now that the engagement should be higher you will need to focus on getting you shift rpm back down where it needs to be. There are many ways to do this. The first thing to try is to add as much weight at the tip of the clutch weight as you may need. If you can't get enough to do the job you could try more in the middle hole but that might be too much for the midrange. Your next options to bring top rpms down would be steeper secondary cam angles and weaker secondary springs. The bigger the number on the angle the more it should lower your rpm, but at some point it may not backshift as well. The mult-angle cams that others here have mentioned can help with the backshift and effect the shift rpm at different speeds. If you are close you may just want to try the weaker secondary spring option with less wrap first. I have kind of listed these things in order of cost to some extent. Buying a bunch of secondary cams can get expensive in a hurry. There is also the option of going to different weights like Heelclickers which work great, are very adjustable, and also are kind of expensive. You would still need to do alot of experimenting with those. It just may be easier to put in and take out screws for the weight adjustments instead of using the Yamaha weights with the rivots. There are many ways to do this . They all take a little experimenting. I definitely believe you need to make sure you can get your engagement where you need it first with the Yamaha weights then go after the rest. If you just get your shift rpm were you want it first everything you do to help your engagement will throw off you shift rpm. ( Last statement does not apply to heel clickers or other adjustable weights.)
