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Are you referring to these gaps here?
If so, know that I had the same thing happen to me. Driftmotion actually has a kit that comes with little extensions for this very reason. I'm not sure why this is the case, but I solved it by buying some really nice spacers from my local Home Depot. It was like 70 bucks and the driftmotion kit is double that I'm pretty sure. This is what mine looks like -
Interesting... and somewhat frustrating findings. Those of us who swap in MKIII R154's always have to do more work all around compared to those with tripod trans swaps.
The way I did this with my MKIII R154 (which I still have installed in my SC) is to use the 1986-1992 MKIII Supra Turbo R154 OEM trans mount which I bolted onto a used 1982-1985 Celica W58 factory crossmember. Only the Celica crossmember doesn't bolt to both sides as it isn't wide enough. I had a shop cut it off on one side with a cutoff wheel tool, bolt both sides up with a trans jack holding the weight of the transmission in the middle and then had them weld plate steel onto the two cut pieces to bridge the space once everything had been verified to be aligned correctly with the tall trans jack. This was all done with the SC on a lift in a shop bay. A coat of black paint was put onto the final extended trans crossmember before bolting it back on.
I'm still using that custom modified 82-85 Celica W58 crossmember today. I had this all done in 2013 long before XCessive Manufacturing made their piece and before Driftmotion made their super too low sitting crossmember for MKIII R154 transmissions.
If you have a JDM Soarer R154 from 1991-1993 or the JDM Soarer/Chaser/MarkII/etc. Tripod R154 then you can bolt in the stock 1995-1997 SC300 M/T, MKIV W58 and Soarer 1994-2000 R154 trans mount and just use an SC300 factory 5-speed trans crossmember.
Looking at the thickness of the XCessive crossmember it seems they did not account for the exact height of the MKIII Supra W58/R154 OEM trans mount. It's a common older style four bolt mounting pattern and it is possible that different applications of mounts for the R-series and W-series transmissions have different height OEM mounts.
That may be why spacers are required in this case. Potentially a different mount that has the in-line trans tail casing bolt holes may be a bit taller or a bit shorter in height which may correct the issue but I haven't tried it yet.
The reason I recommend the XCessive R154 crossmember for MKIII R154 swaps into SC's is that it's very, very difficult to find an 82-85 Celica W58 crossmember these days and it needs to be hacked up and extended with plate steel and a welder anyway. XCessive has at least made something specifically for the SC300/400/Soarer chassis with the older style trans mount bolt holes which does bolt up on each side.
I had thought the worst case issue upon installation might be a slight need to adjust the bolt holes a bit with a drill bit.... but apparently the specific mount used and the height at which the transmission's rear section sits is a problem for some. The XCessive crossmember is still good as an off the shelf starting point for MKIII R154 swappers.
....
Seeing your predicament Joe it might be worth it to try the Driftmotion aftermarket trans mount but I think that does require their super low (too low IMO) MKIII trans aftermarket crossmember which is supposed to go with it.
Some measurements may be in order.
I believe what joewitafro is suggesting is to use the staggered bolt hole style W58/R154 OEM trans mount which is the same as factory 1992-1997 SC300 5-speed OEM trans mounts. The factory manual R154 Soarers all use the same trans mount and crossmember setup as all factory manual SC300 5-speeds.
The early 1992-1994 SC300 5-speeds and early 1991-1993 Soarer 1JZ-GTE R154 5-speed cars both have transmissions from the factory with the old style extended shifter housings (non-tripod) and all use the same transmission tunnels with the same opening placement. The SC300 W58 5-speed went tripod in 1995 and the Soarer 2.5GT 5-speed went tripod in 1994. The MKIV Supra began production with tripod-only transmissions before the luxury coupe siblings got them. All three manual versions of each chassis from the factory used the same OEM trans mounts and crossmembers (except for the MKIV's that got V160's and V161's).
I think dropping the trans a bit lower is the way to go. I think I'll head to a machine shop and get some nice ones made since I am going through all the trouble.
I spent the day working through re-looming the harness. I'd like to clean up under there but wiring is intimidating. I'll start researching what I can delete.
Outside of that, I worked up a prototype of the "retro" shift boot I have been thinking of. I wanted to add my own little spin on my swap.
Been driving this thing roughly 15 miles a day. Short commute to work.
Everything feels good despite the shifter extension being closer to the tunnel than I would like. I get some extra vibrations, but nothing worrisome.
One thing that has happened that I didn't expect. My CEL is cleared. Has anyone experienced this? I originally had code 7.1 but just replaced the Vacuum Modulator last week. Since then no codes whatsoever.
That's a great report s far!! The CEL code 71 going away means you apparently solved the EGR obstruction/flow issue this time. The OBD1 ECUs will clear a trouble code if there is no reoccurrence of the issue after 100 miles at most. Unrelated but when I was chasing an intermittent CEL code 14 "Bad IGF"issue (related to a wiring mistake I made with my GTE engine swap) *those* CEL codes would go in and out almost immediately on the dash.
Whereas with my original engine when I was trying to solve my EGR issue with its CEL code 71 I did have to wait every 100 miles of driving from each attempted fix after having reset the ECU. From a fresh ECU reset 100 miles of driving is what it takes for the computer to exit closed loop mode and go into open loop mode. So after 100 miles from a reset if my attempted fix to the EGR system hadn't yet cleared the obstruction/malfunction then I'd get the CEL 71 back again... and that's when I'd have to try the next fix attempt in the list. Process of elimination.
Just be aware that at least once while you own the SC300 you'll have to clear out the "Y" intake pipe of carbon buildup for the EGR system to flow normally. I made a DIY writeup guide for how to do that whenever the time may come.
For now consider this a win! The CEl 71 went sway after you replaced that vacuum modulator. Sometimes that's all it is... just a single component. Also buy yourself a spare 1992-1997 2JZ-GE EGR VSV in good working condition early just to have it for a rainy day.