Install the transmission into the bellhousing. If the transmission does not seat fully into the bellhousing, do not under any circumstances use bolts to pull it in, as severe damage can result. Allowing the transmission to hang in the clutch assembly while not fully seated to the bellhousing will damage the clutch, transmission, or both. If the clutch was not properly aligned when installed, it may be necessary to reinstall the clutch. Do not let go of the transmission unless you have at least one bolt in and finger tight. After the transmission is seated you can torque the bolts to specification in a cross pattern starting with one of the top bolts first.
With the transmission bolts tight, lift the transmission up high enough to remove the jack under the oil pan. Install the transmission mount to the transmission case and tighten bolts hand tight at this time. Install the crossmember frame brackets to the frame rails and tighten hand tight. Then install the main crossmember tube by adjusting the stainless steel receivers fore and aft until the transmission pad holes are lined up with the crossmember and the crossmember is straight. When satisfied with crossmember position, tighten the frame bracket bolts and stainless steel receiver bolts. Slowly lower the transmission down onto the crossmember and secure the transmission pad to the crossmember. For future removal and installation, the adjustable steel receivers may stay secured and the center section of the crossmember can be dropped out.
Now it's time to climb back inside the car inside and install the shifter mechanism to the transmission using RTV sealant. Aftermarket shifters are also available for the T56. Classic Chevy 5-Speeed recommends B&M or McLeod if you choose to upgrade to an aftermarket shifter.
To cover the access hole in the trans tunnel, cut a piece of suitable sheetmetal to size and either weld in or screw into place.
Because the clutch master cylinder bracket mounts behind the brake master cylinder (to the firewall), you will need to first remove the brake system master cylinder. With the brake master cylinder removed, install the firewall bracket onto the steering column support studs. Insert the clutch master cylinder through the mounting bracket and bolt the master cylinder to the firewall. With some vehicle models, it may be necessary to enlarge the existing clutch pedal pushrod hole in the firewall to accommodate the master cylinder. Make sure the master cylinder clutch pedal pushrod is coming straight out of the master cylinder; mark the location where the pushrod spherical bearing meets the clutch pedal. Remove the clutch pedal from the car. (At this point, it is important to check Classic Chevy's supplemental instructions for proper master cylinder clutch pedal pushrod-to-clutch pedal adjustment.) Using a 5/64-inch drill bit, drill a hole and tap it with a 1/4-inch x 28-thread tap. Alternatively, you can use a bolt and nut instead of tapping and threading this hole. Re-install the clutch pedal and attach the master cylinder pushrod to the clutch pedal. Now you can re-install the brake booster and master cylinder.
Attach the remote mount reservoir in any convenient location on the firewall, as long as the reservoir is above the level of the clutch master cylinder. Attach the quick-connect fitting of the master cylinder fluid line to the throwout bearing. The next step is to bleed the clutch system (use DOT 3 fluid only). You can attempt to bleed the system in the same manner that you would bleed the brake system by pumping the clutch pedal two or three times, holding the pedal down and then opening the bleed screw. Repeat this process until all of the air is out of the system. After the system is properly bled, refill the reservoir to slightly below full.
Remove the rubber shipping-stopper (rubber "donut") that's found on the output shaft of the transmission. Use a pair of pliers and some care when pulling it out gently around in a circle to remove it without damaging the rear seal. To install the driveshaft apply a small amount of grease to the splines of the yolk and slide it onto the output shaft, turning it as you go. Attach the rear U-joint straps and the torque bolts to specification. Make sure the driveshaft has sufficient clearance to rotate and follow suspension travel. Ideally, there will be between 3/4- to 1 1/2-inch of slip-yoke shaft showing past the tip of the output shaft. You should have the rear suspension supported when checking this measurement (in other words the rear suspension should not be hanging down).
Next, install the provided pigtail wiring harnesses into the appropriate receptacles on the transmission. The reverse lock connector (GM #12101857) is often tied into the brake light switch so that you can easily shift the transmission into reverse when the brakes are applied. The VSS connector (GM #88987993) is typically tied into to your engine wiring harness and also operates your electric speedometer gauge. The reverse light connector (GM #12085485) connects into your existing reverse light wiring. The proper method of wiring your T56 depends on which motor you're using, where you purchased the engine, and the type of speedometer you're using. If you're using a stock speedometer, you'll need to purchase a converter box. Before breaking in your T56, it's important to check that you've properly completed your work. Among other checks, make sure that you've tightened all bolts to specifications and completed all electrical connections, filled the transmission with Dexron III transmission fluid, and re-installed the drain plug. Then install the driveshaft at both ends and check for clearance around all moving parts. Now you're ready to start your engine and break in your transmission with the car still on jackstands. With the shifter in neutral, start the engine and allow it to warm up. Listening any for any abnormal noises, test all gears by shifting through each gear using the clutch. Be careful to only shift into reverse at idle. Do this for about 10 minutes. Remove car from jackstands. Testdrive the car at reasonable speeds, eventually increasing rpm and speed. Drive at reasonable levels during the 500-mile break in period. And then drive at unreasonable speeds after it's broken in!