Hard shifting after head gasket replacement.

Well I got the head gaskets and intake finished so no more milk shakes but now when I shift into drive it shifts very hard with a clunk, also when driving I notice it shifting harder while going through the gears. Any idea what may have caused this? The vaccum to the tranny was reconnected btw so I ruled that out. I filled the coolant with just plain water and heard that may cause some sort of sensor to misread and cause this but I cant really see that, i have been wrong before though..lol. Another thing it is doing is if I rev it to say 3 grand while in park it gives out a loud snap noise from under the hood, cant seem to find exactly where, i thought maybe a backfire or something from the exhaust but it sounds more mechanical, hoping it isnt the bottom end letting go. When i first start it now and then it lets out some bumps, ticks and knocks from what sounds like down below for a few seconds but then stops. Doesnt do it all the time. Can I put 100% lucas motor oil in the crank or would it be better to mix it with normal oil? I hear lucas is awesome after work like this. I have 4 quarts of Formula 1 synthentic also. I need to change the oil in the next few days so was just wondering. Thanks for any input.

please re-post year, model and engine size.

please re-post year, model and engine size.
94 Gran Prix SE 3100

Only put 1 quart of Lucas in. It is very thick and will blow your motor if you use 5 qts of it.
Your ECM has a rev limiter that will kick in around 3500-4000 rpm's in park to protect the engine, which may be your issue there, especially if the engine stumbles at the same time you hear the noise.
On the trans issue, water is thinner than antifreeze, and doesn't pick up heat properly, so the CTS may not read correctly. This WILL cause the car to shift differently. Try shifting the car manually, if it shifts ok that way, you may need a trans vacuum modulator.

Take out that little vacuum one way thing (I cant think what its called right now) down on the vacuum line by the modulator and just put a rubber line one between the steel line and the modulator and see what happens.