I owned 2 of GM's 2.8 V6. The 3.1 V6 is of similar design.

Now that the heads are off, take these to a motor shop and have a valve job done especially if the engine has 100,000 miles or more. If you don't do this, at least check for worn valve guides. Replace any bad guides and reseat the valves. Change out the valve seals. Replace any valve springs that are shorter than the service limit. New valve springs would be good.

The main problem that I had with both of my V6s was the intake manifold coming loose. When this happens, it will leak coolant into the oil pan, and may develop an air leak and lean out one or more cylinders.

When you put the intake manifold back on, take more than normal care in tightening the bolts. Once the bolts snug up, begin tightening using the recomended sequence but do not turn any nut more than 1/2 turn during the initial tightening. Go through the bolt pattern as many times as needed. Once the bolts begin to become tight, tighten only 1/4 turn while moving through the bolt pattern. Continue until the bolts arrive at the specified torque.

Contine putting other things back together, but do not cover up the access to the intake bolts. After 1/2, re-torque the intake bolts. You should not disturb the manifold much after the 1/2 hr period because of the RTV sealant used at the corners of the maniflod where it meets the block. Its best not to disturb the sealant after it passes into its set-up phase. The intake manifold also serves as the valley cover.

Use the best RTV you can find. It must be rated hot-oil resistant, will not harm the catalytic converter, and be non-acidic. It should also have the highest tmeperature rating that you can get.

Don't bother putting the intake back on until you have hot-oil resistant RTV, or the recommended sealant.

Check the cam lobes and followers/lifters for wear. If significant wear is present, replace the cam shaft and lifters.

Check the cam shaft and crank for end play. If excessive, remedy.

Check the oil pump and refresh as needed.

Now that you are this far into the engine, you may as well look at the timing chain. Replace if play exceeds the service limit.