Well, from what I've read, as the timing chain tensioner gets worse it will start to make noise all the time. Some never go bad, some do. The big thing is to use 5-30 oil, from what I understand the V-6's are even more sensitive to this, but my wifes 01 XL-7 doesn't make any noise, mine did from when I first got it. It never got worse, it's just here and there. Try not to go over 2500 to 3000 rpms when cold, let it warm up just a couple of minutes before you drive it, that helps.
About the 5 speed, buddy, I feel your pain. I noticed it on my test drive and thought that the previous owner was a little hard on it, but in fact, it's just the way it is. I usually double clutch to drop down to 4th from 5th. If I am going 45 mph or less I usually don't have to. IT can grind going into 3rd, the best thing to do is just to upshift easy, never force it and it's fine. 1st can be hard to get into if your stopped, I just slip it in first while rolling up to a stop.
I've found to tranny to be happy shifting at 3500 rpm, also get better gas milage if you go easy on the throttle and let it rev to 3500 rpm before shifting. Works better than short shifting. My only complaint with the gearing is the space between 1st and 2nd gear, all the other gears are pretty evenly spaced. The longer space between 1st and 2nd gear make it a little tougher to get it going up hill, especially when your having to granny shift it all the time. I used GM synthetic gear oil which they recomended and I thought it helped a little bit with the shifting.
HTH
Dave