I say do it!! lol i love 2dr's and did the same thing, bought a $500 2dr 2wd that needed a clutch then bought a parts jeep for 300 that didnt run, another 300 for a 4x4 AX15 and bam i got a 4x4 plus alot of extra parts that ive been selling to make some money back.
Any cheap vehicle you buy will need repairs and if i had the choice of paying 3k for mine with all ive done to it or 3k for a slightly nicer STOCK jeep, id take mine any day of the week.
Project/DD - 95' Cherokee Sport, 2 Door, Converted to 4x4, AX-15, NP231, Black and lots of other goodies
88' Cherokee Limited - RIP
Sold - 96' Cherokee Sport 4x4, 2 Door, AW4, NP242, Its the girlfriends now!!