Sir the EE90 DX, TX and XE Saloon had a 4 speed manual and 3 speed A/T with 2E Electronic carb engine 73PS 1.3L.
The TX 4WD with 1.6L EFI 4AFE 100PS had only a 5 speed M/T and XE Saloon 4WD had an option of 4 speed A/T as well.
SE and SE Limited with 1.5L 5AFE 94PS and top model SE Limited G 1.5L 5AFHE 105PS had 5 speed M/T and 4 speed A/T.
The Diesel engine was 1CIII 1.8L with 67PS, all diesel variants whether DX or SE limited were 5 speed manual and 4 speed A/T.
The Indus Corolla is better, will cost more, try to find the 1.6 GLi 95-97 A/T.
The Indus XE and GL had the same 2E 1.3L carb with the difference in equipment like power windows and mirrors.
Indus 2.0D, 2.0D limited also had different equipment with a newer 2.0L 2C engine with 73PS.
The Indus GLi and SE Limited had a 1.6L EFi 4AFE.
All Indus Corolla had 5 speed M/T or a 4 speed A/T.
A/T was only available in Gli and SE variants with no option in diesel engines.
The JDM E100 and local SE Limited models are insanely expensive and a waste of money.
Local SE and SE Limited were announced in end of 1999 as a 2000 (Millennium model), same 4AFE engine but with alloys, wooden dash panels and and optional S/R, production stopped in 2002 with the intro of E120 Xli shape Corolla.
The JDM models DX had a 4EFE 1.3L EFi with 100PS and 4 speed manual.
The E100 JDM SE limited had alloys, S/R, ABS, Airbags and power everything with a 5AFE.
The Top GT models also had 1.6L 4AGE with 160PS (only seen 1 car of that model in Pakistan).
Both cars are very similar, but E100 is better in drive and ride.
E90 has cheap parts.
A Top E90 will cost you 400K to 480K.
A local Indus will cost 680K for nice Gli or SE and 600K for 98-00 GL.
A Top JDM E100 will cost you 800K to even north of 1M PKR.
What is your budget?
After studying all my life about these cars I concluded that there is nothing special in E90 or E100 apart from cheap parts and service that consequently adds to its resale.
A 3G Accord or a 6th Gen Civic is a much better car to own and drive.