A couple things could be happening here, some of this advice is theoretical.
1. Even when the starter switch is bypassed the NSS (neutral safety switch) needs to be "tricked" or bypassed by jumping some wires on the harness. Lots of write-ups online on how to do this. Without these wires jumped the computer doesn't know you're trying to start the engine.
2. There are two types of cam pickups, the jumping wires with the crank sensor only works up 96'. The 97+ has a different magnet configuration for the cam pickup.
3. 4 cylinder models have have 3 sets of 3 notches on the flexplate for the computer to read vs 3 sets of 4 notches for the six cylinder computer.

My theory is emulate the stock setup as close as possible, if this is accomplished and it still doesn't work the problem is most likely a loose or cut ground wire somewhere as many of these sensors share a ground.

 

Updates. Trans, new torque converter and tcase back together. The 1-2 harsh shift has been corrected. I asked my transmission man to replace the 1-2 accumulator spring with the factory one. When I got it back he explained that the spring alone would change almost nothing so they also changed the throttle valve and 1-2 servo. The new FTI 2600 stall converter is perfect for this combo.... Between the trans and torque converter it now shifts and accelerates like a dream.
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New urethane transmission mount and hydraulic motor mounts worked out perfectly.

Fabricated a cold air intake. Also new gauges. The trans temp never goes over 200* even without lockup. Vacuum gauge reads 22mmhg at idle which is really excellent.

I'll post pics soon.

 

http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141102_112327_zpskmfouuan.jpg.htmlRedesigned hydraulic mounts

http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141115_105122_zpsw1i2i397.jpg.html
http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141115_105231_zpsftgf4yir.jpg.htmlCut and turned arms to match angle of engine

http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141106_072044_zpsvhgxwsmm.jpg.html
http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141102_164118_zpsu2vggx6k.jpg.html
http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141109_170336_zpsgpv5qpqn.jpg.html
http://s508.photobucket.com/user/evenglass1/media/Mobile%20Uploads/20141109_195122_zps42mjdhdc.jpg.html

 

are those mounts the 2859's?. Both of my converted xj's used the OE Benz mounts, and they both crushed/settled. Maybe it is because I did not use the little shock absorber.
Let us know how the new mounts work out? I ordered some special 4cyl diesel mounts, from Brandon Products. I will not use the MB mounts again. If these don't work, I will rebuild my mounts to use the Ranger 2698's

 

2993, about $25 a piece $18 Rock Auto. 2001 5.7 corvette mounts. They are very stout but handle the vibrations very well, I'd run them again. http://www.summitracing.com/parts/ani-2993

 

http://s508.photobucket.com/user/evenglass1/media/10622854_405834922915374_1115729623113589963_n_zpse438e5c3.jpg.html
http://s508.photobucket.com/user/evenglass1/media/1482910_405834896248710_6020963998516421728_n_zps167ef779.jpg.html
http://s508.photobucket.com/user/evenglass1/media/10458450_405834952915371_5828590201940364115_n_zps70656a82.jpg.html
99-01' dual 12 blade electric fans. These things move some real air, about 4300 CFM.

 

Just wondering what the height and diameter of the corvette mount is. I just checked the ford ranger mount and the parts store and it measures 3" tall and 4" dia. My mercedes mounts are to soft . Did you notice less vibration with corvette mounts. Thanks

 

The Corvette mounts have been one of the most worthwhile upgrades. They are hydraulic and internally regulated and strong. They vibrated more at first then settled down after 500miles, they vibrate just slightly more than the Mercedes mush mounts. I'll measure them when I get a chance and post it up.

 

How did you make the brackets inside the engine bay?

 

I engineered it from the block out toward the frame. Hang the engine from a cherry picker mark the frame where the center of the arm would connect to the engine on both sides. Build the mount bucket at the height and size needed for the motor mount. measure from center of motor mount to engine block and design arm to connect mount to block.