You are going to have to check the TCM to ECU connections.

To Get the instructions on how to do this download the JTIS from the stickies or the manual from Jagrepair.com and go to pinpoint test E.

This will hopefully tell you what is wrong.

 

If you download the manual start at page 2843

 

UPDATE: Replaced the 5 year old battery after testing this morning at 12.3V Automatically got a gearbox fault and restricted performance message along with a couple misfires upon startup. Drive to my shop in limp mode and misfires became worse. Having it tested now. Pray for me the issue lies within bad coils.

 

Can you DIY. If so buy yourself an elm 327 and download the manual a misfire can be caused by a lot of simple things that you could have checked yourself and saved a lot of money.

These cars are not cheap if you keep on going to a workshop and the costs for labour can easily go over the value of the car. Even though it could be a classic one day

 

$37 to have them scan it. Coil #6 was bad. Replaced it myself, $50 all is well now. Runs, drives and shift fine aside from my usual lurch. LET IT BE KNOW FOR FUTURE REFERENCE that a faulty coil, even though engine seems to run fine and has no CEL, CAN cause the transmission issues described in this thread!

 

Good news but still buy yourself an elm They only cost around 10 dollars. It will allow you scan the engine and some other parts yourself.

 

Probably would have thrown a code in time but sooner fixed the better.

+1 get a code & scan tool - elm327 is a great cheap one

 

I just like how I never even felt the miss let alone get a code until after I replaced the battery.

 

It should have shown a code for this problem but it may not have had a chance too because as you have already said at the start of the post you kept on disconnecting the battery to try and sort out the gearbox problem. This would have cleared all of the codes.

 

Particularly, cleared the counters it needs for misfires and the values for such as fuel trims.

The PCM can detect problems such as misfires typically long before they can be felt.

This means that usually the problem can be fixed cheaply before serious damage occurs that would be expensive to fix. (E.g. changing one bad coil soon after it went bad is cheaper than changing it but also having to change the cat conv!)

 

This may sound insane, I had problems with the car dropping gear in the middle of an intersection a while ago. Always had problems with first gear. If I could get past first I was fine. Anyway, a dozen repair shops, including Jag, told me I needed a new transmission. I new that was crap so I just kept troubleshooting and driving it. As is turns out, a failing ignition coil was creating somesort of CAN feedback that messed with the transmission computer. The reason I bring this up is that I had exactly the pump noise you are describing. It was kind of a light pump whine that pulse at irregular intervals and was very hard to hear. I think it had something to do with the computer regulating pressure from the transmission front pump. But after I changed the ignition coil, no more shifting issues or pump noise. Point being that it could very well be computer/valve body related.